3BVH Blood Clotting date Jan 07, 2008
title Crystal Structure Of Recombinant Gammad364a Fibrinogen Fragm The Peptide Ligand Gly-Pro-Arg-Pro-Amide
authors S.R.Bowley, B.K.Merenbloom, L.Betts, N.Okumura, A.Heroux, O.V.Gor S.T.Lord
compound source
Molecule: Fibrinogen Alpha Chain
Chain: A, D
Fragment: Residues 148-209
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Gene: Fga
Expression_system: Cricetulus Griseus
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pmlp

Molecule: Fibrinogen Beta Chain
Chain: B, E
Fragment: Residues 191-488
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Gene: Fgb
Expression_system: Cricetulus Griseus
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pmlp

Molecule: Fibrinogen Gamma Chain
Chain: C, F
Fragment: Residues 128-420
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Gene: Fgg
Expression_system: Cricetulus Griseus
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pmlp

Molecule: 4-Mer Peptide Gprp
Chain: G, I, H, J
Engineered: Yes

Synthetic: Yes
Other_details: Synthetic Peptide
symmetry Space Group: P 21 21 21
R_factor 0.220 R_Free 0.260
crystal
cell
length a length b length c angle alpha angle beta angle gamma
89.844 94.913 225.754 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.60 Å
ligand CA, FUC, NAG enzyme
Primary referencePolymerization-defective fibrinogen variant gammaD364A binds knob "A" peptide mimic., Bowley SR, Merenbloom BK, Okumura N, Betts L, Heroux A, Gorkun OV, Lord ST, Biochemistry. 2008 Aug 19;47(33):8607-13. Epub 2008 Jul 22. PMID:18642883
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (232 Kb) [Save to disk]
  • Biological Unit Coordinates (3bvh.pdb1.gz) 215 Kb
  • Biological Unit Coordinates (3bvh.pdb2.gz) 162 Kb
  • LPC: Ligand-Protein Contacts for 3BVH
  • CSU: Contacts of Structural Units for 3BVH
  • Likely Quarternary Molecular Structure file(s) for 3BVH
  • Structure Factors (571 Kb)
  • Retrieve 3BVH in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3BVH from S2C, [Save to disk]
  • Re-refined 3bvh structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3BVH 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 3BVH
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3BVH, from MSDmotif at EBI
  • Fold representative 3bvh from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3bvh_C] [3bvh_E] [3bvh_F] [3bvh_B] [3bvh_J] [3bvh_H] [3bvh_G] [3bvh_I] [3bvh_A] [3bvh] [3bvh_D]
  • SWISS-PROT database: [P02671] [P02675] [P02679]
  • Domain organization of [FIBA_HUMAN] [FIBB_HUMAN] [FIBG_HUMAN] by SWISSPFAM
  • Domain found in 3BVH: [FBG ] by SMART
  • Other resources with information on 3BVH
  • Community annotation for 3BVH 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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