3FIB Blood Coagulation date Jul 14, 1997
title Recombinant Human Gamma-Fibrinogen Carboxyl Terminal Fragment (Residues 143-411) Bound To Calcium At Ph 6.0: A Further Refinement Of Pdb Entry 1fib, And Differs From 1fib By The Modelling Of A Cis Peptide Bond Between Residues K338 And C339
authors K.P.Pratt, H.C.F.Cote, D.W.Chung, R.E.Stenkamp, E.W.Davie
compound source
Molecule: Fibrinogen Gamma Chain Residues
Chain: A
Fragment: Residues 143 - 411
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Organ: Blood
Expression_system: Pichia Pastoris
Expression_system_taxid: 4922
Expression_system_strain: Gs115
Expression_system_plasmid: Ppic9k
symmetry Space Group: P 1 21 1
R_factor 0.154 R_Free 0.206
crystal
cell
length a length b length c angle alpha angle beta angle gamma
37.530 68.420 47.670 90.00 105.36 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand CA enzyme
related structures by homologous chain: 1FIB
Primary referenceThe primary fibrin polymerization pocket: three-dimensional structure of a 30-kDa C-terminal gamma chain fragment complexed with the peptide Gly-Pro-Arg-Pro., Pratt KP, Cote HC, Chung DW, Stenkamp RE, Davie EW, Proc Natl Acad Sci U S A 1997 Jul 8;94(14):7176-81. PMID:9207064
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (48 Kb) [Save to disk]
  • Biological Unit Coordinates (3fib.pdb1.gz) 44 Kb
  • LPC: Ligand-Protein Contacts for 3FIB
  • CSU: Contacts of Structural Units for 3FIB
  • Likely Quarternary Molecular Structure file(s) for 3FIB
  • Retrieve 3FIB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3FIB from S2C, [Save to disk]
  • View 3FIB 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 3FIB
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3FIB, from MSDmotif at EBI
  • Genome occurence of 3FIB's fold from GeneCensus
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d3fib__, region [Jmol] [rasmolscript] [script source]
  • Fold representative 3fib from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3fib_A] [3fib]
  • SWISS-PROT database: [P02679]
  • Domain organization of [FIBG_HUMAN] by SWISSPFAM
  • Domain found in 3FIB: [FBG ] by SMART
  • Alignments of the sequence of 3FIB with the sequences similar proteins can be viewed for 3FIB's classification [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 [FIBG_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 3FIB
  • Community annotation for 3FIB 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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