1n73: Difference between revisions
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|PDB= 1n73 |SIZE=350|CAPTION= <scene name='initialview01'>1n73</scene>, resolution 2.90Å | |PDB= 1n73 |SIZE=350|CAPTION= <scene name='initialview01'>1n73</scene>, resolution 2.90Å | ||
|SITE= | |SITE= | ||
|LIGAND= <scene name='pdbligand= | |LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene> | ||
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
|DOMAIN= | |||
|RELATEDENTRY=[[1lwu|1LWU]], [[1fzc|1FZC]], [[1fzf|1FZF]], [[1n86|1N86]], [[1n8e|1N8E]] | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1n73 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n73 OCA], [http://www.ebi.ac.uk/pdbsum/1n73 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1n73 RCSB]</span> | |||
}} | }} | ||
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[[Category: Pandi, L.]] | [[Category: Pandi, L.]] | ||
[[Category: Yang, Z.]] | [[Category: Yang, Z.]] | ||
[[Category: | [[Category: isopeptide cross-linked chain]] | ||
[[Category: | [[Category: protein-peptide complex]] | ||
''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 22:26:20 2008'' | ||
Revision as of 22:26, 30 March 2008
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| , resolution 2.90Å | |||||||
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| Ligands: | , | ||||||
| Related: | 1LWU, 1FZC, 1FZF, 1N86, 1N8E
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| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Fibrin D-Dimer, Lamprey complexed with the PEPTIDE LIGAND: GLY-HIS-ARG-PRO-AMIDE
OverviewOverview
The crystal structure of fragment double-D from factor XIII-cross-linked lamprey fibrin has been determined at 2.9 A resolution. The 180 kDa covalent dimer was cocrystallized with the peptide Gly-His-Arg-Pro-amide, which in many fibrinogens, but not that of lamprey, corresponds to the B-knob exposed by thrombin. The structure was determined by molecular replacement, a recently determined structure of lamprey fragment D being used as a search model. GHRPam was found in both the gamma- and beta-chain holes. Unlike the situation with fragment D, the crystal packing of the cross-linked double-D structure exhibits two different D-D interfaces, each gamma-chain facing gamma-chains on two other molecules. One of these (interface I) involves the asymmetric interface observed in all other D fragments and related structures. The other (interface II) encompasses a completely different set of residues. The two abutments differ in that interface I results in an "in line" arrangement of abutting molecules and the interface II in a "zigzag" arrangement. So far as can be determined (the electron density could only be traced on one side of the cross-links), it is the gamma-chains of the newly observed zigzag units (interface II) that are joined by the reciprocal epsilon-amino-gamma-glutamyl cross-links. Auspiciously, the same novel D-D interface was observed in two lower-resolution crystal structures of human double-D preparations that had been crystallized under unusual circumstances. These observations show that double-D structures are linked in a way that is sufficiently flexible to accommodate different D-D interfaces under different circumstances.
About this StructureAbout this Structure
1N73 is a Protein complex structure of sequences from Petromyzon marinus. Full crystallographic information is available from OCA.
ReferenceReference
The crystal structure of fragment double-D from cross-linked lamprey fibrin reveals isopeptide linkages across an unexpected D-D interface., Yang Z, Pandi L, Doolittle RF, Biochemistry. 2002 Dec 31;41(52):15610-7. PMID:12501189
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