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 Diffraction	resolution	2.60 Å
ligand	CA, FUC, NAG	enzyme
Gene Ontology	Chain Function Process Component E, B eukaryotic cell surface bind... chaperone binding platelet degranulation blood coagulation hemostasis platelet activation response to calcium ion extracellular region fibrinogen complex extracellular space plasma membrane cell cortex external side of plasma memb... platelet alpha granule platelet alpha granule lumen... blood microparticle F, C eukaryotic cell surface bind... metal ion binding platelet degranulation blood coagulation hemostasis platelet activation response to calcium ion extracellular region fibrinogen complex extracellular space plasma membrane cell cortex external side of plasma memb... platelet alpha granule platelet alpha granule lumen... blood microparticle
Primary reference	Polymerization-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 (581 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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

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_A] [3bvh_B] [3bvh_C] [3bvh_D] [3bvh_E] [3bvh_F] [3bvh_G] [3bvh_H] [3bvh_I] [3bvh_J] SWISS-PROT database: [P02671] [P02675] [P02679] Domain organization of [FIBA_HUMAN] [FIBB_HUMAN] [FIBG_HUMAN] by SWISSPFAM Domain found in 3BVH: [FBG ] by SMART Alignments of the sequence of 3BVH with the sequences similar proteins can be viewed for 3BVH's classification [FIBA_HUMAN] [FIBB_HUMAN] [FIBG_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list. A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [FIBA_HUMAN] [FIBB_HUMAN] [FIBG_HUMAN] at ProtoMap. Click on the Cluster number.

Other resources with information on 3BVH

Community annotation for 3BVH at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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