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 Diffractionresolution 2.90 Å
ligand BMA, CA, GAL, MAN, NAG, NDG, SIA enzyme
Gene
Ontology
ChainFunctionProcessComponent
F, C, I, L


K, E, B, H


Primary referenceCrystal 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 (1834 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.
  • 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_B] [3ghg_G] [3ghg] [3ghg_E] [3ghg_S] [3ghg_L] [3ghg_T] [3ghg_I] [3ghg_J] [3ghg_C] [3ghg_M] [3ghg_D] [3ghg_N] [3ghg_R] [3ghg_A] [3ghg_P] [3ghg_K] [3ghg_F] [3ghg_Q] [3ghg_O] [3ghg_H]
  • SWISS-PROT database: [P02671] [P02675] [P02679]
  • Domain organization of [FIBA_HUMAN] [FIBB_HUMAN] [FIBG_HUMAN] by SWISSPFAM
  • Domains found in 3GHG: [FBG] [Fib_alpha ] 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)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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