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PDBsum entry 2ffd

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protein ligands metals Protein-protein interface(s) links
Blood clotting PDB id
2ffd
Jmol
Contents
Protein chains
65 a.a. *
303 a.a. *
298 a.a. *
57 a.a. *
Ligands
GLY-PRO-ARG-VAL ×4
NAG-NAG-FUC ×2
Metals
_CA ×4
Waters ×231
* Residue conservation analysis
PDB id:
2ffd
Name: Blood clotting
Title: Fibrinogen fragment d with "a" knob peptide mimic gprvve
Structure: Fibrinogen alpha/alpha-e chain. Chain: a, d. Fragment: residues 145-210. Engineered: yes. Fibrinogen beta chain. Chain: b, e. Fragment: residues 179-491. Engineered: yes. Fibrinogen gamma chain.
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: fga. Expressed in: cricetulus griseus. Expression_system_taxid: 10029. Expression_system_cell_line: ovary cells. Gene: fgb. Gene: fgg.
Biol. unit: Pentamer (from PQS)
Resolution:
2.89Å     R-factor:   0.214     R-free:   0.268
Authors: L.Betts
Key ref: L.Betts et al. (2006). The structure of fibrinogen fragment D with the 'A' knob peptide GPRVVE. J Thromb Haemost, 4, 1139-1141. PubMed id: 16689770
Date:
19-Dec-05     Release date:   04-Jul-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P02671  (FIBA_HUMAN) -  Fibrinogen alpha chain
Seq:
Struc:
 
Seq:
Struc:
866 a.a.
65 a.a.
Protein chains
Pfam   ArchSchema ?
P02675  (FIBB_HUMAN) -  Fibrinogen beta chain
Seq:
Struc:
491 a.a.
303 a.a.
Protein chains
Pfam   ArchSchema ?
P02679  (FIBG_HUMAN) -  Fibrinogen gamma chain
Seq:
Struc:
453 a.a.
298 a.a.
Protein chain
Pfam   ArchSchema ?
P02671  (FIBA_HUMAN) -  Fibrinogen alpha chain
Seq:
Struc:
 
Seq:
Struc:
866 a.a.
57 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     fibrinogen complex   1 term 
  Biological process     signal transduction   3 terms 
  Biochemical function     receptor binding     2 terms  

 

 
J Thromb Haemost 4:1139-1141 (2006)
PubMed id: 16689770  
 
 
The structure of fibrinogen fragment D with the 'A' knob peptide GPRVVE.
L.Betts, B.K.Merenbloom, S.T.Lord.
 
  ABSTRACT  
 
No abstract given.

 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20484082 S.E.Stabenfeldt, J.J.Gossett, and T.H.Barker (2010).
Building better fibrin knob mimics: an investigation of synthetic fibrin knob peptide structures in solution and their dynamic binding with fibrinogen/fibrin holes.
  Blood, 116, 1352-1359.  
19650644 S.R.Bowley, N.Okumura, and S.T.Lord (2009).
Impaired protofibril formation in fibrinogen gamma N308K is due to altered D:D and "A:a" interactions.
  Biochemistry, 48, 8656-8663.
PDB code: 3hus
17208341 A.S.Wolberg (2007).
Thrombin generation and fibrin clot structure.
  Blood Rev, 21, 131-142.  
17982313 D.K.Galanakis, M.Neerman-Arbez, T.Scheiner, A.Henschen, D.Hubbs, C.Nagaswami, and J.W.Weisel (2007).
Homophenotypic Aalpha R16H fibrinogen (Kingsport): uniquely altered polymerization associated with slower fibrinopeptide A than fibrinopeptide B release.
  Blood Coagul Fibrinolysis, 18, 731-737.  
16940416 R.I.Litvinov, O.V.Gorkun, D.K.Galanakis, S.Yakovlev, L.Medved, H.Shuman, and J.W.Weisel (2007).
Polymerization of fibrin: Direct observation and quantification of individual B:b knob-hole interactions.
  Blood, 109, 130-138.  
17414213 S.T.Lord (2007).
Fibrinogen and fibrin: scaffold proteins in hemostasis.
  Curr Opin Hematol, 14, 236-241.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.