3GHG	Blood Clotting	date	Mar 03, 2009
title	Crystal Structure Of Human Fibrinogen
authors	R.F.Doolittle, J.M.Kollman, M.R.Sawaya, L.Pandi, M.Riley
compound		source
Molecule: Fibrinogen Alpha Chain Chain: A, D, G, J Fragment: Mature Chain Synonym: Fibrinopeptide A		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Tissue: Blood Plasma
Molecule: Fibrinogen Beta Chain Chain: B, E, H, K Fragment: Mature Chain Synonym: Fibrinopeptide B		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Tissue: Blood Plasma
Molecule: Fibrinogen Gamma Chain Chain: C, F, I, L Fragment: Mature Chain		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Tissue: Blood Plasma
Molecule: A Knob Chain: M, N, Q, R Engineered: Yes		Synthetic: Yes
Molecule: B Knob Chain: O, P, S, T Engineered: Yes		Synthetic: Yes
symmetry	Space Group: P 1 21 1	R_factor 0.252 R_Free 0.309
crystal cell	length a length b length c angle alpha angle beta angle gamma 135.238 94.866 300.812 90.00 94.81 90.00
method	X-Ray Diffraction	resolution	2.90 Å
ligand	BMA, CA, GAL, MAN, NAG, NDG, SIA	enzyme
Gene Ontology	Chain Function Process Component F, C, I, L 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 K, E, B, H 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
Primary reference	Crystal structure of human fibrinogen., Kollman JM, Pandi L, Sawaya MR, Riley M, Doolittle RF, Biochemistry. 2009 May 12;48(18):3877-86. PMID:19296670

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (670 Kb) [Save to disk] Biological Unit Coordinates (3ghg.pdb1.gz) 327 Kb Biological Unit Coordinates (3ghg.pdb2.gz) 329 Kb LPC: Ligand-Protein Contacts for 3GHG CSU: Contacts of Structural Units for 3GHG Likely Quarternary Molecular Structure file(s) for 3GHG Structure Factors (1881 Kb) Retrieve 3GHG in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3GHG from S2C, [Save to disk] Re-refined 3ghg structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3GHG 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 3GHG

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 3GHG, from MSDmotif at EBI Fold representative 3ghg from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3ghg_A] [3ghg_B] [3ghg_C] [3ghg_D] [3ghg_E] [3ghg_F] [3ghg_G] [3ghg_H] [3ghg_I] [3ghg_J] [3ghg_K] [3ghg_L] [3ghg_M] [3ghg_N] [3ghg_O] [3ghg_P] [3ghg_Q] [3ghg_R] [3ghg_S] [3ghg_T] SWISS-PROT database: [P02671] [P02675] [P02679] Domain organization of [FIBA_HUMAN] [FIBB_HUMAN] [FIBG_HUMAN] by SWISSPFAM Domain found in 3GHG: [FBG ] by SMART Alignments of the sequence of 3GHG with the sequences similar proteins can be viewed for 3GHG'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 3GHG

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

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