1b5g: Difference between revisions
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|PDB= 1b5g |SIZE=350|CAPTION= <scene name='initialview01'>1b5g</scene>, resolution 2.07Å | |PDB= 1b5g |SIZE=350|CAPTION= <scene name='initialview01'>1b5g</scene>, resolution 2.07Å | ||
|SITE= <scene name='pdbsite=CAT:Active+Site'>CAT</scene> | |SITE= <scene name='pdbsite=CAT:Active+Site'>CAT</scene> | ||
|LIGAND= <scene name='pdbligand=NA:SODIUM+ION'>NA</scene> | |LIGAND= <scene name='pdbligand=BCC:6-AMINO-6-BENZYL-5-OXO-OCTAHYDRO-INDOLIZINE-3-CARBALDEHYDE'>BCC</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=THZ:BENZOTHIAZOLE'>THZ</scene>, <scene name='pdbligand=TYS:SULFONATED+TYROSINE'>TYS</scene> | ||
|ACTIVITY= [http://en.wikipedia.org/wiki/Thrombin Thrombin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.5 3.4.21.5] | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Thrombin Thrombin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.5 3.4.21.5] </span> | ||
|GENE= | |GENE= | ||
|DOMAIN= | |||
|RELATEDENTRY= | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1b5g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b5g OCA], [http://www.ebi.ac.uk/pdbsum/1b5g PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1b5g RCSB]</span> | |||
}} | }} | ||
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==Overview== | ==Overview== | ||
The X-ray crystal structures of four beta-strand-templated active site inhibitors of thrombin containing P1' groups have been determined and refined at about 2.1-A resolution to crystallographic R-values between 0.148 and 0.164. Two of the inhibitors have an alpha-ketoamide functionality at the scissile bond; the other two have a nonhydrolyzable electrophilic group at the P1' position. The binding of lysine is compared with that of arginine at the S1 specificity site, while that of D,L-phenylalanine enantiomorphs is compared in the S3 region of thrombin. Four different P1' moieties bind at the S1' subsite in three different ways. The binding constants vary between 2.0 microM and 70 pM. The bound structures are used to intercorrelate the various binding constants and also lead to insightful inferences concerning binding at the S1' site of thrombin. | The X-ray crystal structures of four beta-strand-templated active site inhibitors of thrombin containing P1' groups have been determined and refined at about 2.1-A resolution to crystallographic R-values between 0.148 and 0.164. Two of the inhibitors have an alpha-ketoamide functionality at the scissile bond; the other two have a nonhydrolyzable electrophilic group at the P1' position. The binding of lysine is compared with that of arginine at the S1 specificity site, while that of D,L-phenylalanine enantiomorphs is compared in the S3 region of thrombin. Four different P1' moieties bind at the S1' subsite in three different ways. The binding constants vary between 2.0 microM and 70 pM. The bound structures are used to intercorrelate the various binding constants and also lead to insightful inferences concerning binding at the S1' site of thrombin. | ||
==About this Structure== | ==About this Structure== | ||
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[[Category: Kahn, M.]] | [[Category: Kahn, M.]] | ||
[[Category: Tulinsky, A.]] | [[Category: Tulinsky, A.]] | ||
[[Category: complex (serine protease/inhibitor)]] | [[Category: complex (serine protease/inhibitor)]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 18:54:02 2008'' | ||
Revision as of 18:54, 30 March 2008
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| , resolution 2.07Å | |||||||
|---|---|---|---|---|---|---|---|
| Sites: | |||||||
| Ligands: | , , , | ||||||
| Activity: | Thrombin, with EC number 3.4.21.5 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
HUMAN THROMBIN COMPLEXED WITH NOVEL SYNTHETIC PEPTIDE MIMETIC INHIBITOR AND HIRUGEN
OverviewOverview
The X-ray crystal structures of four beta-strand-templated active site inhibitors of thrombin containing P1' groups have been determined and refined at about 2.1-A resolution to crystallographic R-values between 0.148 and 0.164. Two of the inhibitors have an alpha-ketoamide functionality at the scissile bond; the other two have a nonhydrolyzable electrophilic group at the P1' position. The binding of lysine is compared with that of arginine at the S1 specificity site, while that of D,L-phenylalanine enantiomorphs is compared in the S3 region of thrombin. Four different P1' moieties bind at the S1' subsite in three different ways. The binding constants vary between 2.0 microM and 70 pM. The bound structures are used to intercorrelate the various binding constants and also lead to insightful inferences concerning binding at the S1' site of thrombin.
About this StructureAbout this Structure
1B5G is a Protein complex structure of sequences from Hirudo medicinalis and Homo sapiens. Full crystallographic information is available from OCA.
ReferenceReference
Bound structures of novel P3-P1' beta-strand mimetic inhibitors of thrombin., St Charles R, Matthews JH, Zhang E, Tulinsky A, J Med Chem. 1999 Apr 22;42(8):1376-83. PMID:10212123
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