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<applet load='Dnac_from_2ggz_a.pdb' size='500' frame='true' align='right'
<StructureSection load='' size='350' side='right' caption='' scene=''>
scene='User:Eric_Martz/Sandbox_4/Dnac_model_from_2ggz_a/6' />
==Homology Model of DnaC==
The following sequence was provided for DnaC from E. coli:


<tt>
*1 <scene name='31/319439/Surface_test/1'>Surface test 1</scene>: simple surface on chain A of 1d66. Colored translucent green. This surface was generated with the '''representations''' tab of the SAT.
MKNVGDLMQR LQKMMPAHIK PAFKTGEELL AWQKEQGAIR SAALERENRA
<br>
MKMQ<b>RTFNRS GIRPLHQNCS FENYRVECEG QMNALSKARQ YVEEFDGNIA
<br>
SFIFSGKPGT GKNHLAAAIC NELLLRGKSV LIITVADIMS AMKDTFRNSG
<br>
TSEEQLLNDL SNVDLLVIDE IGVQTESKYE KVIINQIVDR RSSSKRPTGM
<br>
LTNSNMEEMT KLLGERVMDR MRLGNSLWVI FNWDSYR</b>SRV TGKEY
</tt>


This sequence was submitted to Swiss Model, which [http://tinyurl.com/4nek2q generated the homology model] shown here (<scene name='User:Eric_Martz/Sandbox_4/Dnac_model_from_2ggz_a/6'>restore initial scene</scene>) using [[2qgz]] chain A as a template, which has 18.6% sequence identity. Apparently Swiss Model used predicted secondary structure to help in the sequence alignment, but details are not clear to me. The homology model represents residues 55-237, shown in boldface in the above sequence. ''Because of the low sequence identity, this model may well contain major errors, or even be wholly incorrect.''


Swiss Model has apparently used the [[temperature value]] field in the PDB file to indicate regions that are highly unreliable, namely the regions that are <font color="red"><b>red</b></font> when the model is <scene name='User:Eric_Martz/Sandbox_4/Dnac_model_from_2ggz_a/4'>colored by temperature</scene>. These regions are shown as '''translucent white''' in the initial scene (using the Jmol command <i>select temperature >50</i>). The uncertainty in three of these regions is explained by gaps in the template model (see below). Although the details of these regions are even more uncertain than other regions, it seems likely that these loops are on the surface, if the homology model turns out to be substantially correct.
*2 <scene name='31/319439/6zgi_translucen_backbone/1'>6zgi as translucent backbone, chain colors</scene> (no isosurfaces). After clicking this standard SAT-generated green link, then
<jmol>
<jmolButton>
<script>
isosurface delete; isosurface "http://proteopedia.org/wiki/images/6/67/6zgi-cavities.jvxl";
</script>
<text>Load isosurface cavities</text>
</jmolButton>
</jmol>
(From uploaded file http://proteopedia.org/wiki/images/6/67/6zgi-cavities.jvxl -- see [[Image:6zgi-cavities.jvxl]])


The [[Conservation, Evolutionary|evolutionary conservation]] pattern, revealed by ConSurf, is quite interesting, showing <scene name='User:Eric_Martz/Sandbox_4/Dnac_model_from_2ggz_a/7'>two conserved patches</scene>.<ref>ConSurf found only 10 sequences in SwissProt, with an Average Pairwise Distance of 1.6. The [http://consurf.tau.ac.il/results/1222995227/output.html run shown here] used 100 sequences from Uniprot, with an APD of 1.4.</ref>


In order to find specific residues, or see charge distribution or other aspects of this homology model, please use:
*3 <jmol>
<jmolButton>
<script>
load "http://proteopedia.org/wiki/images/c/c6/6zgi-cavities.pngj";
</script>
<text>Load .PNGJ file</text>
</jmolButton>
</jmol>
(From uploaded file http://proteopedia.org/wiki/images/c/c6/6zgi-cavities.pngj -- see [http://proteopedia.org/wiki/index.php/Image:6zgi-cavities.pngj Image:6zgi-cavities.png])


[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=http%3A//proteopedia.org/wiki/images/3/3e/Dnac_from_2ggz_a.pdb View DnaC Homology Model in FirstGlance in Jmol]


==Crystal Structure of DnaC==
*4 <jmol>
<jmolLink>
<script>
load "http://proteopedia.org/wiki/images/c/c6/6zgi-cavities.pngj";
</script>
<text>Green link loading uploaded PNGJ file</text>
</jmolLink>
</jmol>. SAT not involved. PNGJ file generated externally in the [[Jmol/Application|Jmol Java application]], then uploaded to Proteopedia as for the previous item above.


A sequence-based search at the international [http://targetdb.pdb.org/ Structural Genomics TargetDB] reveals that the closest completed structure is 2QGZ, the one chosen by SwissModel as a template. A number of crystal and NMR structures have sequence identities up to 37% but over shorter stretches, and with higher E values.


Diffraction data have been obtained (but the solved structure not yet deposited) for a ''Listeria monocytogenes'' sequence of 307 residues, pI 5.2, with an E value of 1.6e-05, though only 21% sequence identity. Diffraction-quality crystals (but not yet diffraction data) have not been obtained for any sequence with such a low E value.
*5 <scene name='31/319439/6zgi_cavities_from_pngj/1'>Test dropping pngj with cavities into SAT</scene>, then saving scene. (No molecule loaded with the SAT "load molecule" tab.)


''E. coli'' dnaC (245 residues, pI 9.4) has been crystallized by RIKEN Structural Genomics Initiative (Japan), but the crystals may not be of diffraction quality. It has been cloned, expressed as a soluble protein, and purified (but not yet crystallized) by 3 Structural Genomics Groups (RIKEN Structural Genomics Initiative (Japan), Montreal-Kingston Bacterial Structural Genomics Initiative, Midwest Center for Structural Genomics), as have several proteins with >40% sequence identity. So there is reason for optimism that either a crystal structure, or a more suitable template for homology modeling, will be forthcoming soon. One might consider contacting the groups who have reported purification of dnaC to inquire about progress, and possibly request priority for dnaC.


==Gaps in the Template Model==
Tested in Firefox (current version) on macOS Mojave, mid-2014 MacBook Pro, 2.2 GHz Intel Core i7.
<applet load='Dnac_from_2ggz_a.pdb' size='500' frame='true' align='right'
scene='User:Eric_Martz/Sandbox_4/2qgz/3' />
The template was 2QGZ (<scene name='User:Eric_Martz/Sandbox_4/2qgz/3'>initial scene</scene>). The portion of the template used was Glu107-Arg300. Only the amino-terminal 6 residues were not used as template (translucent). Note that there are <scene name='User:Eric_Martz/Sandbox_4/2qgz/5'>three loops</scene> in this segment of the template that lack coordinates due to [[disorder]] in the crystal (marked with spacefilled alpha-carbon atoms).


The missing loops are 202-205 (NGSV), 226-231 (EQATSW), and 268-275 (TIKGSDET). These gaps, which occur between the residues marked /\ below, were apparently ignored in making the model, which has a continuous main chain.
*6 <scene name='31/319439/6zgi_cavities/1'>Cavities in coronavirus spike protein 6zgi</scene>. It took 8.5 min to generate the cavity isosurfaces after I entered the command "isosurface minset 100 interior cavity 3.0 10.0" into the command slot in the SAT. (This command takes ~45 sec in the Jmol Java app which is therefore 11-fold faster for this operation.) After clicking this green link, I waited 11 min and the scene still did not appear. So I think the isosurfaces are being generated again when the green link is clicked.


Below is the alignment produced by Swiss Model, used in making the 3D model. Vertical bars for identity were inserted by hand (I may have missed some).
<pre>
                                                |    | |  |    ||
TARGET    55            R TFNRSGIRPL HQNCSFENYR VECEGQMNAL SKARQYVEEF
2qgzA    100  qkqaais--e riqlvslpks yrhihlsdid vnnasrmeaf saildfveqy
                                                                     
TARGET                    sssss    h h            hhhhhhh hhhhhhhhh
2qgzA              hhh  h  sss    h h            hhhhhhh hhhhhhhhh


                            |        | ||  ||    | |              |
TARGET    96    DGN-IASFIF SGKPGTGKNH LAAAICNELL L-RGKSVLII TVADIMSAMK
2qgzA    148  psaeqkglyl ygdmgigksy llaamahels ekkgvsttll hfpsfaidvk
                                                                     
TARGET                ssss ss    hhh hhhhhhhhhh h h  ssss sshhhhhhh
2qgzA                ssss ss    hhh hhhhhhhhhh hh    ssss sshhhhhhh


                                  ||  |  | ||                |
</StructureSection>
TARGET    144  DTFRNSGTSE EQLLNDLSNV DLLVIDEIGV QTESKYEKVI INQIVDRRSS
2qgzA    198  naiske---- --eidavknv pvlilddiga vrde-----v lqvilqyrml
                  /\                          / \
TARGET                        hhh    ssssss              hhhhhhhhhh
2qgzA                        hh  h    ssssss              hhhhhhhhhh
 
                  |    |                ||| |  |              |
TARGET    194  SKRPTGMLTN SNMEEMTKLL ---GERVMDR MRLGNSLWVI FNWDSYR 
2qgzA    247  eelptfftsn ysfadlerkw awqakrvmer vr-ylarefh leganrr- 
                                      /\
TARGET          h  ssssss    hhhhh          hhhh hh  ssssss s       
2qgzA          h  ssssss    hhhh          hhhh hh hh ssss s
</pre>
 
Below is the sequence with ATOM records (coordinates) from 2QGZ, numbered 100-300, showing the gaps as "...". This sequence listing was used to locate the positions marked /\ above.
<pre>
    1 .......... .......... .......... .......... ..........
  51 .......... .......... .......... .......... .........Q
  101 KQAAISERIQ LVSLPKSYRH IHLSDIDVNN ASRMEAFSAI LDFVEQYPSA
  151 EQKGLYLYGD MGIGKSYLLA AMAHELSEKK GVSTTLLHFP SFAIDVKNAI
  201 S....KEEID AVKNVPVLIL DDIGA..... .VRDEVLQVI LQYRMLEELP
 
  251 TFFTSNYSFA DLERKWA... .....WQAKR VMERVRYLAR EFHLEGANRR
</pre>
(Copied from Protein Explorer's sequence display.)
 
Below is the alignment of dnaC with 2QGZ according to TargetDB (see above).
<pre>
Target Query Results
There are 16 sequences that match your request.
 
 
 
ID:  DR58    Latest update:  2007-09-21    E Value:  0.00028:  view alignment
Lab:  Northeast Structural Genomics Consortium
Name:  Putative primosome component (Helicase loader).
Status:  Selected, Cloned, Expressed, Soluble, Purified, Crystallized, Diffraction, Crystal Structure, In PDB
URL:
http://spine.nesg.org/target.cgi?id=DR58
Database Reference:    PDB: 2QGZ  PFAM: PF07319  MEGA: 3.40.50.300 
Source Organism:    Streptococcus pyogenes
Sequence:
MEKIGETMAKLGQNTRVNSDQLIQTILADPEVASFISQHHLSQEQINLSLSKFNQFLVERQ
KYQLKDPSYIAKGYQPILAMNEGYADVSYLETKELVEAQKQAAISERIQLVSLPKSYRHI
HLSDIDVNNASRMEAFSAILDFVEQYPSAEQKGLYLYGDMGIGKSYLLAAMAHELSEKKG
VSTTLLHFPSFAIDVKNAISNGSVKEEIDAVKNVPVLILDDIGAEQATSWVRDEVLQVIL
QYRMLEELPTFFTSNYSFADLERKWATIKGSDETWQAKRVMERVRYLAREFHLEGANRR
Domain Annotation:    Pfam
Other Sources:
Superfamily | TIGR Families | ProDom | iProClass | Prosite
Protein Properties:
Number of Residues Mol. Weight Avg. Hydropathy Score Charge pI Value
300 34146 -0.321 -4.5 5.4
ID:  hso002001071.2    Latest update:  2008-09-07    E Value:  0.14:  view alignment
Lab:  RSGI
Status:  Selected, Cloned, Expressed, Soluble, Purified, NMR Assigned, HSQC, NMR Structure, In PDB
Database Reference:    PDB: 2EAO 
Source Organism:    Homo sapiens
Sequence:
SQPLLDRSIPDFTAFTTVDDWLSAIKMVQYRDSFLTAGFTSLQLVTQMTSEDLLRIGITLA
GHQKKILNSIHSMRVQISQSPTAMA
Domain Annotation:    Pfam
Other Sources:
Superfamily | TIGR Families | ProDom | iProClass | Prosite
Protein Properties:
Number of Residues Mol. Weight Avg. Hydropathy Score Charge pI Value
86 9585 0.056 1.0 7.7
ID:  NYSGXRC-10353u    Latest update:  2007-03-09    E Value:  0.69:  view alignment
Lab:  SGX Pharmaceuticals
Name:  Q4QL22_HAEI8
Status:  Selected, Cloned, Expressed, Soluble, Purified, Crystallized, Diffraction, Native diffraction-data, Phasing diffraction-data, In PDB
Database Reference:    PDB: 3BGE  BIG: BIG_278  UNIPROT: Q4QL22_HAEI8 
Source Organism:    Haemophilus influenzae
Sequence:
MSNLNFDFAENDFRPLAAKMRPTNLEQYFGQSHLIGEGKPLRKAIQAGHIHSMILWGPPGT
GKTTLAEIIAQRINAEVERISAVTSGIKEIREAIDRAKQNRLADRKTILFVDEVHRFNKS
QQDAFLPHIEDGTVIFIGATTENPSFELNNALLSRARVYVLKSLTTAEIEQVLQQAVEDP
ERGLGKERLILEENLLQVLAEYVNGDARLALNCLELMVDMADEMENGKKIDRTLLKEVLG
ERQARFDKQGDRFYDLISALHKSVRGSAPDAALYWYARILTAGGDPLYVARRLLAIASED
VGNADPRAMQVALAAWDCFTRVGAYEGERAIAQAIIYLAVAPKSNAVYTAFNTAKQQAKD
LPDYDVPPHLRNAPTNLMKELGYGAEYRYAHDEPNAYAAGENYFPPELKDTQYYFPTNRG
MEIQIKEKLERLREQDKSTVKKRYK
Domain Annotation:    Pfam
Other Sources:
Superfamily | TIGR Families | ProDom | iProClass | Prosite
Protein Properties:
Number of Residues Mol. Weight Avg. Hydropathy Score Charge pI Value
446 50278 -0.436 -1.0 6.3
ID:  hsi002013839.1    Latest update:  2008-09-07    E Value:  0.9:  view alignment
Lab:  RSGI
Status:  Selected, Cloned, Expressed, Soluble, Purified, NMR Assigned, HSQC, NMR Structure, In PDB
Database Reference:    PDB: 2EEE 
Source Organism:    Homo sapiens
Sequence:
GSRITYVKGDLFACPKTDSLAHCISEDCRMGAGIAVLFKKKFGGVQELLNQQKKSGEVAVL
KRDGRYIYYLITKKRASHKPTYENLQKSLEAMKSHCLKNGVTDLSMPRIGCGLDRLQWEN
VSAMIEEVFEATDIKITVYTL
Other Sources:
Pfam |  Superfamily | TIGR Families | ProDom | iProClass | Prosite
Protein Properties:
Number of Residues Mol. Weight Avg. Hydropathy Score Charge pI Value
142 15951 -0.273 7.5 9.2
ID:  GO.36728    Latest update:  2008-01-14    E Value:  0.95:  view alignment
Lab:  CESG
Name:  BC011709
Status:  Selected, Expressed, Purified, NMR Assigned, HSQC, NMR Structure, In PDB, Other
Database Reference:    PDB: 2JYC 
Source Organism:    Homo sapiens
Sequence:
MASSLNEDPEGSRITYVKGDLFACPKTDSLAHCISEDCRMGAGIAVLFKKKFGGVQELLNQ
QKKSGEVAVLKRDGRYIYYLITKKRASHKPTYENLQKSLEAMKSHCLKNGVTDLSMPRIG
CGLDRLQWENVSAMIEEVFEATDIKITVYTL
Other Sources:
Pfam |  Superfamily | TIGR Families | ProDom | iProClass | Prosite
Protein Properties:
Number of Residues Mol. Weight Avg. Hydropathy Score Charge pI Value
152 17025 -0.319 4.5 8.5
ID:  NYSGXRC-10354e    Latest update:  2008-03-19    E Value:  1.6:  view alignment
Lab:  SGX Pharmaceuticals
Name:  Q7V3J8_PROMP
Status:  Selected, Cloned, Expressed, Soluble, Purified, Crystallized, Diffraction, Native diffraction-data, Phasing diffraction-data, In PDB
Database Reference:    PDB: 3CTD  BIG: BIG_278  UNIPROT: Q7V3J8_PROMP 
Source Organism:    Prochlorococcus marinus
Sequence:
MESDNLFSNTYRIESNAPLADKLRPKNLDDFFGQESILGHDSLLRNAILNDKVGNIIFSGP
PGVGKTTLIEIISSNTRSSLIKLNAVLSSIKELRTEIANAKERLRSSNRKTILFIDEVHR
FTSVQQDALLPSIENGTITFIGATTENPFFAVNKALISRARIFSLLPLNKNDLKKIIDKV
IKYYSCLKDSKVVEIKEEAINHLIKFSGGDARNLINALELGISITKENKENLVVIDLAIA
EDSIQKKNIVYDKNGQNHFDVISAFIKSIRGSDPDATLYWLANMVEAGEDPNFIFRRLLI
SACEDIGLADPNAIVVVQSCCDAFDRVGFPEGLFFLSQASLYLAISPKSNSTKSIFKALE
AIKATNVSLVPNHLKNNASNYLNPHNYQGKWLQQEYLPTDLQGIKFWKPKDSGWEKNKYE
DLPKKQKS
Domain Annotation:    Pfam
Other Sources:
Superfamily | TIGR Families | ProDom | iProClass | Prosite
Protein Properties:
Number of Residues Mol. Weight Avg. Hydropathy Score Charge pI Value
429 48010 -0.245 6.0 8.5
ID:  SR1    Latest update:  2008-05-05    E Value:  1.9:  view alignment
Lab:  Northeast Structural Genomics Consortium
Name:  Putative sigma L-dependent transcriptional regulator yplP.
Status:  Selected, Cloned, Expressed, Soluble, Purified, HSQC, In PDB, Work Stopped
URL:
http://spine.nesg.org/target.cgi?id=SR1
Database Reference:    PDB: 1XYZ  MEGA: 1.10.8.60  MEGA: 3.40.50.300 
Source Organism:    Bacillus subtilis
Sequence:
MNSAPKLNTFQHLIGEHQTFLEAKRIAKQFSLSELPVLITGKIGTGKNHFAHAIHLESSRS
NEPFISVNCSTHSEETLIHELFGPNGNTGVFQKAVRGTLFLDDVWRMPASVQAQLLKALD
SDTEKPRMICASADRSVEHTFRQDLFYRLNILTLTLPELSERKSDIPLLTQHFLSNSGQQ
LLIDPSVFPVLEKHAFEGNVRELKNAADYMAAVSSGGTIQPYDLPPYIRGTIDGKTSKKK
AKLLTLMEKAEFLFILETIKVLNEKGEPASRRIISEHSKNTQTSLTPQQVRSRLDYLEKK
DYVTKSRGRAGTKITFEGLSFIETLKNQMI
Domain Annotation:    Pfam
Other Sources:
Superfamily | TIGR Families | ProDom | iProClass | Prosite
Protein Properties:
Number of Residues Mol. Weight Avg. Hydropathy Score Charge pI Value
331 37210 -0.358 10.5 9.5
ID:  APC90123.1    Latest update:  2007-03-01    E Value:  2.4:  view alignment
Lab:  Midwest Center for Structural Genomics
Name:  PG0945
Status:  Selected, Cloned, Expressed, Soluble, Purified, Crystallized, Diffraction-quality Crystals, Diffraction, Crystal Structure, In PDB
Remark:
ABC transporter, permease protein, putative (gi 34397011) ; targeted domain 44...183
Database Reference:    PDB: 2P0S  NCBI: AAQ66075.1  NCBI TAXONOMY DB: 242619 
Source Organism:    Porphyromonas gingivalis W83
Sequence:
QLGGDMKTIAIADRTGEYEQLFKENDEFRFVHAEKTAEEYRKMGADKSGIDAVLEIRQDLL
EDPNAVAIYGYKQLPASVSNHISRILSDYLSDKKIASYNIPDIKQILADSKIELSVHTYK
WSEDGTNERTSGELASGIS
Other Sources:
Pfam |  Superfamily | TIGR Families | ProDom | iProClass | Prosite
Protein Properties:
Number of Residues Mol. Weight Avg. Hydropathy Score Charge pI Value
140 15687 -0.571 -6.5 4.6
ID:  NYSGXRC-10108a    Latest update:  2006-10-13    E Value:  2.9:  view alignment
Lab:  SGX Pharmaceuticals
Name:  PRPR_ECOLI
Status:  Selected, Cloned, Expressed, Soluble, Purified, Crystallized, Diffraction, Native diffraction-data, Phasing diffraction-data, In PDB
Database Reference:    PDB: 2PJU  PFAM: PF06506  UNIPROT: P77743 
Source Organism:    Escherichia coli
Sequence:
MAHPPRLNDDKPVIWTVSVTRLFELFRDISLEFDHLANITPIQLGFEKAVTYIRKKLANER
CDAIIAAGSNGAYLKSRLSVPVILIKPSGYDVLQALAKAGKLTSSIGVVTYQETIPALVA
FQKTFNLRLDQRSYITEEDARGQINELKANGTEAVVGAGLITDLAEEAGMTGIFIYSAAT
VRQAFSDALDMTRMSLRHNTHDATRNALRTRYVLGDMLGQSPQMEQVRQTILLYARSSAA
VLIEGETGTGKELAAQAIHREYFARHDARQGKKSHPFVAVNCGAIAESLLEAELFGYEEG
AFTGSRRGGRAGLFEIAHGGTLFLDEIGEMPLPLQTRLLRVLEEKEVTRVGGHQPVPVDV
RVISATHCNLEEDMQQGRFRRDLFYRLSILRLQLPPLRERVADILPLAESFLKVSLAALS
APFSAALRQGLQASETVLLHYDWPGNIRELRNMMERLALFLSVEPTPDLTPQFMQLLLPE
LARESAKTPAPRLLTPQQALEKFNGDKTAAANYLGISRTTFWRRLKS
Domain Annotation:    Pfam
Other Sources:
Superfamily | TIGR Families | ProDom | iProClass | Prosite
Protein Properties:
Number of Residues Mol. Weight Avg. Hydropathy Score Charge pI Value
528 58649 -0.135 7.5 8.4
ID:  sto001002459.2    Latest update:  2008-09-07    E Value:  3.4:  view alignment
Lab:  RSGI
Status:  Selected, Cloned, Expressed, Soluble, Purified, Crystallized, Diffraction-quality Crystals, Native diffraction-data, Phasing diffraction-data, Crystal Structure, In PDB
Database Reference:    PDB: 2Z0M 
Source Organism:    Sulfolobus tokodaii
Sequence:
MNEKIEQAIREMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILELGMKSLV
VTPTRELTRQVASHIRDIGRYMDTKVAEVYGGMPYKAQINRVRNADIVVATPGRLLDLWS
KGVIDLSSFEIVIIDEADLMFEMGFIDDIKIILAQTSNRKITGLFSATIPEEIRKVVKDF
ITNYEEIEACIGLANVEHKFVHVKDDWRSKVQALRENKDKGVIVFVRTRNRVAKLVRLFD
NAIELRGDLPQSVRNRNIDAFREGEYDMLITTDVASRGLDIPLVEKVINFDAPQDLRTYI
HRIGRTGRMGRKGEAITFILNEYWLEKEVKKVSQKA
Domain Annotation:    Pfam
Other Sources:
Superfamily | TIGR Families | ProDom | iProClass | Prosite
Protein Properties:
Number of Residues Mol. Weight Avg. Hydropathy Score Charge pI Value
337 38342 -0.210 9.0 9.8
ID:  ttk003000125.1    Latest update:  2008-09-07    E Value:  3.5:  view alignment
Lab:  RSGI
Status:  Selected, Cloned, Expressed, Soluble, Purified, Crystallized, Diffraction-quality Crystals, Native diffraction-data, Phasing diffraction-data, Crystal Structure, In PDB
Database Reference:    PDB: 2YWS 
Source Organism:    Thermus thermophilus
Sequence:
MKGMFTPGNGPVQISAEAIKKRVEELGGEIARDYQGKTPHLICVLNGAFIFMADLVRAIPL
PLTMDFIAISSYGNAFKSSGEVELLKDLRLPIHGRDVIVVEDIVDTGLTLSYLLDYLEAR
KPASVRVAALLSKPSRRQVEVPIHYLGFEIEDAYVYGYGLDRAQFDRNLPFITSIRPEEE
Domain Annotation:    Pfam
Other Sources:
Superfamily | TIGR Families | ProDom | iProClass | Prosite
Protein Properties:
Number of Residues Mol. Weight Avg. Hydropathy Score Charge pI Value
181 20170 0.022 -3.5 5.1
ID:  ttk003000125.3    Latest update:  2008-09-07    E Value:  3.5:  view alignment
Lab:  RSGI
Status:  Selected, Cloned, Expressed, Soluble, Purified, Crystallized, Diffraction-quality Crystals, Native diffraction-data, Phasing diffraction-data, Crystal Structure, In PDB
Database Reference:    PDB: 2YWU 
Source Organism:    Thermus thermophilus
Sequence:
MKGMFTPGNGPVQISAEAIKKRVEELGGEIARDYQGKTPHLICVLNGAFIFMADLVRAIPL
PLTMDFIAISSYGNAFKSSGEVELLKDLRLPIHGRDVIVVEDIVDTGLTLSYLLDYLEAR
KPASVRVAALLSKPSRRQVEVPIHYLGFEIEDAYVYGYGLDRAQFDRNLPFITSIRPEEE
Domain Annotation:    Pfam
Other Sources:
Superfamily | TIGR Families | ProDom | iProClass | Prosite
Protein Properties:
Number of Residues Mol. Weight Avg. Hydropathy Score Charge pI Value
181 20170 0.022 -3.5 5.1
ID:  ttk003000125.2    Latest update:  2008-09-07    E Value:  3.5:  view alignment
Lab:  RSGI
Status:  Selected, Cloned, Expressed, Soluble, Purified, Crystallized, Diffraction-quality Crystals, Native diffraction-data, Phasing diffraction-data, Crystal Structure, In PDB
Database Reference:    PDB: 2YWT 
Source Organism:    Thermus thermophilus
Sequence:
MKGMFTPGNGPVQISAEAIKKRVEELGGEIARDYQGKTPHLICVLNGAFIFMADLVRAIPL
PLTMDFIAISSYGNAFKSSGEVELLKDLRLPIHGRDVIVVEDIVDTGLTLSYLLDYLEAR
KPASVRVAALLSKPSRRQVEVPIHYLGFEIEDAYVYGYGLDRAQFDRNLPFITSIRPEEE
Domain Annotation:    Pfam
Other Sources:
Superfamily | TIGR Families | ProDom | iProClass | Prosite
Protein Properties:
Number of Residues Mol. Weight Avg. Hydropathy Score Charge pI Value
181 20170 0.022 -3.5 5.1
ID:  AtR62    Latest update:  2005-05-16    E Value:  4.7:  view alignment
Lab:  Northeast Structural Genomics Consortium
Name:  Hypothetical protein Atu3015 (AGR_L_3574p).
Status:  Selected, Cloned, Expressed, Soluble, Purified, Crystallized, Diffraction, HSQC, Crystal Structure, In PDB
URL:
http://spine.nesg.org/target.cgi?id=AtR62
Database Reference:    PDB: 1ZP6  MEGA: 3.40.50.300 
Source Organism:    Agrobacterium tumefaciens
Sequence:
MNMTDDLGGNILLLSGHPGSGKSTIAEALANLPGVPKVHFHSDDLWGYIKHGRIDPWLPQS
HQQNRMIMQIAADVAGRYAKEGYFVILDGVVRPDWLPAFTALARPLHYIVLRTTAAEAIE
RCLDRGGDSLSDPLVVADLHSQFADLGAFEHHVLPVSGKDTDQALQSAINALQSGRFRID
AS
Other Sources:
Pfam |  Superfamily | TIGR Families | ProDom | iProClass | Prosite
Protein Properties:
Number of Residues Mol. Weight Avg. Hydropathy Score Charge pI Value
183 19929 -0.098 -1.5 6.2
ID:  BSGCAIR31267    Latest update:  2006-08-16    E Value:  7.1:  view alignment
Lab:  Berkeley Structural Genomics Center
Status:  Selected, Cloned, Expressed, Soluble, Purified, Crystallized, Diffraction-quality Crystals, Diffraction, Crystal Structure, In PDB
Database Reference:    PDB: 2HQB 
Source Organism:    Bacillus halodurans
Sequence:
MVGLLVEDTIDDQGWNRKAYEGLLNIHSNLDVDVVLEEGVNSEQKAHRRIKELVDGGVNLI
FGHGHAFAEYFSTIHNQYPDVHFVSFNGEVKGENITSLHFEGYAMGYFGGMVAASMSETH
KVGVIAAFPWQPEVEGFVDGAKYMNESEAFVRYVGEWTDADKALELFQELQKEQVDVFYP
AGDGYHVPVVEAIKDQGDFAIGYVGDQADLGGSTILTSTVQHVDDLYVLVAKRFQEGKLE
SGNLYYDFQDGVVSLGEFSSVVPDEVREQITDAISTYIQTGQFPHEEER
Domain Annotation:    Pfam
Other Sources:
Superfamily | TIGR Families | ProDom | iProClass | Prosite
Protein Properties:
Number of Residues Mol. Weight Avg. Hydropathy Score Charge pI Value
290 32294 -0.260 -26.5 4.2
ID:  356698    Latest update:  2004-11-04    E Value:  8.3:  view alignment
Lab:  JCSG
Status:  Selected, Cloned, Expressed, Purified, Crystallized, Diffraction-quality Crystals, Diffraction, Crystal Structure, In PDB
Remark:
Accession:2649494 lacc:TB0541B Start:1 End:180;status_date::2008-10-01:3
Database Reference:    PDB: 2ISB 
Protein Name:
gi|11498698|ref|NP_069927.1| fumarase (fum-1) [Archaeoglobus fulgidus DSM 4304]
Source Organism:    ARCHAEOGLOBUS FULGIDUS
Sequence:
MVMEYELRTPLVKDQILKLKVGDVVYITGEIFTARDEAHARALEWMEEGKELPFSFDKGVV
YHCGPLVKKNDEWRVVSAGPTTSARMNPFTPKILEKVECMGIIGKGGMSEEVVEAMRGKA
AYFAFTGGAGALAAMSIKKVKGVVWEDLGMPEAVWLLEVERFGPCIVAIDAHGNSLYRR
Database Reference:    NCBI REFSEQ: NP_069927.1 
Domain Annotation:    Pfam
Other Sources:
Superfamily | TIGR Families | ProDom | iProClass | Prosite
Protein Properties:
Number of Residues Mol. Weight Avg. Hydropathy Score Charge pI Value
180 19926 -0.008 -0.5 6.3
 
 
ID:  DR58  Center: NESGC
E-value: 0.00028  Identity: 19.737%
 
                                    10        20        30       
Query                        MKNVGDLMQRLQKMMPAHIKPAFKTGEELLAWQKEQGA
                                    Q+ Q  P++I  +++    +    + +
Subjct EVASFISQHHLSQEQINLSLSKFNQFLVERQKYQLKDPSYIAKGYQPILAMNEGYADVSY
              40        50        60        70        80        90
 
      40        50        60        70        80        90       
Query  IRSAALERENRAMKMQRTFNRSGIRPLHQNCSFENYRVECEGQMNALSKARQYVEEF-DG
      +++  L + ++  +++ ++  ++  +++  + +  V+  ++M+A+S  ++VE++ ++
Subjct LETKELVEAQKQAAISERIQLVSLPKSYRHIHLSDIDVNNASRMEAFSAILDFVEQYPSA
              100      110      120      130      140      150
 
      100      110      120        130      140      150     
Query  NIASFIFSGKPGTGKNHLAAAICNELLLR-GKSVLIITVADIMSAMKDTFRNSGTSEEQL
      +  ++ + G  G GK++L AA+ +EL  + G S+ ++  ++  +K+++ N++++EE 
Subjct EQKGLYLYGDMGIGKSYLLAAMAHELSEKKGVSTTLLHFPSFAIDVKNAISNGSVKEE--
              160      170      180      190      200         
 
        160      170        180      190      200      210   
Query  LNDLSNVDLLVIDEIGV-QTESKYEKVIINQIVDRRSSSKRPTGMLTNSNMEEMTK----
      ++ ++NV +L++D+IG+ Q+ S  +  +++ I++ R  + PT + +N ++ ++ +   
Subjct IDAVKNVPVLILDDIGAEQATSWVRDEVLQVILQYRMLEELPTFFTSNYSFADLERKWAT
      210      220      230      240      250      260       
 
                    220      230      240   
Query  LLG-------ERVMDRMRLGNSLWVIFNWDSYRSRVTGKEY
      + G      +RVM+R+R                     
Subjct IKGSDETWQAKRVMERVRYLAREFHLEGANRR       
      270      280      290      300       
</pre>
 
==Notes==
<references />
Retrieved from "https://proteopedia.openfox.io/w/User:Eric_Martz/Cavities_tests"