1SDD Blood Clotting date Feb 13, 2004
title Crystal Structure Of Bovine Factor Vai
authors T.E.Adams, M.F.Hockin, K.G.Mann, S.J.Everse
compound source
Molecule: Coagulation Factor V
Chain: A
Fragment: A1 Domain (Residues 29-305)
Synonym: Activated Protein C Cofactor
Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913
Other_details: Purified From Plasma

Molecule: Coagulation Factor V
Chain: B
Fragment: Light Chain (A3, C1, C2 Domains, Residues 1565-22
Synonym: Activated Protein C Cofactor

Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913
Other_details: Purified From Plasma
symmetry Space Group: P 21 21 21
R_factor 0.252 R_Free 0.296
crystal
cell
length a length b length c angle alpha angle beta angle gamma
63.370 86.560 229.200 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand CA, CU, NAG enzyme
note 1SDD is a representative structure
related structures by homologous chain: 1CZV
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceThe crystal structure of activated protein C-inactivated bovine factor Va: Implications for cofactor function., Adams TE, Hockin MF, Mann KG, Everse SJ, Proc Natl Acad Sci U S A 2004 Jun 15;101(24):8918-23. Epub 2004 Jun 7. PMID:15184653
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (152 Kb) [Save to disk]
  • Biological Unit Coordinates (1sdd.pdb1.gz) 146 Kb
  • LPC: Ligand-Protein Contacts for 1SDD
  • CSU: Contacts of Structural Units for 1SDD
  • Likely Quarternary Molecular Structure file(s) for 1SDD
  • Structure Factors (213 Kb)
  • Retrieve 1SDD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1SDD from S2C, [Save to disk]
  • Re-refined 1sdd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1SDD in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 1SDD
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1SDD, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1sdda1, region A:1-180 [Jmol] [rasmolscript] [script source]
        - Domain d1sdda2, region A:181-296 [Jmol] [rasmolscript] [script source]
        - Domain d1sddb1, region B:1657-1723 [Jmol] [rasmolscript] [script source]
        - Domain d1sddb2, region B:1724-1862 [Jmol] [rasmolscript] [script source]
        - Domain d1sddb3, region B:1863-2024 [Jmol] [rasmolscript] [script source]
        - Domain d1sddb4, region B:2025-2182 [Jmol] [rasmolscript] [script source]
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1sdd_A] [1sdd] [1sdd_B]
  • SWISS-PROT database: [Q28107]
  • Domain organization of [FA5_BOVIN] by SWISSPFAM
  • Domain found in 1SDD: [FA58C ] by SMART
  • Other resources with information on 1SDD
  • Community annotation for 1SDD at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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