PDBsum entry 1lwu

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protein ligands metals Protein-protein interface(s) links
Blood clotting PDB id
Protein chains
99 a.a. *
315 a.a. *
317 a.a. *
NH2 ×4
NDG ×8
MAN ×8
NAG ×4
BMA ×3
_CA ×8
* Residue conservation analysis
PDB id:
Name: Blood clotting
Title: Crystal structure of fragment d from lamprey fibrinogen comp the peptide gly-his-arg-pro-amide
Structure: Fibrinogen alpha-1 chain. Chain: a, d, g, j. Fragment: fragment. Fibrinogen beta chain. Chain: b, e, h, k. Fragment: segment 2 of 2. Fibrinogen gamma chain. Chain: c, f, i, l. Ligand gly-his-arg-pro-nh2.
Source: Petromyzon marinus. Sea lamprey. Organism_taxid: 7757. Synthetic: yes
Biol. unit: Octamer (from PQS)
2.80Å     R-factor:   0.245     R-free:   0.287
Authors: Z.Yang,G.Spraggon,L.Pandi,S.J.Everse,M.Riley,R.F.Doolittle
Key ref:
Z.Yang et al. (2002). Crystal structure of fragment D from lamprey fibrinogen complexed with the peptide Gly-His-Arg-Pro-amide. Biochemistry, 41, 10218-10224. PubMed id: 12162736 DOI: 10.1021/bi020299t
03-Jun-02     Release date:   23-Aug-02    
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Protein chains
Pfam   ArchSchema ?
P02674  (FIBA1_PETMA) -  Fibrinogen alpha-1 chain (Fragment)
966 a.a.
99 a.a.*
Protein chains
P02678  (FIBB_PETMA) -  Fibrinogen beta chain (Fragments)
477 a.a.
315 a.a.
Protein chains
Pfam   ArchSchema ?
P04115  (FIBG_PETMA) -  Fibrinogen gamma chain
432 a.a.
317 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 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  


DOI no: 10.1021/bi020299t Biochemistry 41:10218-10224 (2002)
PubMed id: 12162736  
Crystal structure of fragment D from lamprey fibrinogen complexed with the peptide Gly-His-Arg-Pro-amide.
Z.Yang, G.Spraggon, L.Pandi, S.J.Everse, M.Riley, R.F.Doolittle.
The crystal structure of fragment D from lamprey fibrinogen has been determined at 2.8 A resolution. The 89 kDa protein was cocrystallized with the peptide Gly-His-Arg-Pro-amide, which in many fibrinogens-but not lamprey-corresponds to the B knob exposed by thrombin. Because lamprey fragment D is more than 50% identical in sequence with human fragment D, the structure of which has been reported previously, it was possible to use the method of molecular replacement. The space group of the lamprey crystals is P1; there are four molecules in the unit cell. Although the fragments are packed head to head by the same D:D interface as is observed in other related preparations containing fragments D, the tails are uniquely joined by an unnatural association of the terminal sections of the residual coiled coils from adjacent molecules. Some features of the lamprey structure are clearer than have been observed in previous fragment D structures, including the beta-chain carbohydrate cluster, for one, and the important gamma-chain carboxyl-terminal segment, for another. The most significant differences between the lamprey and human structures occur in connecting loops at the entryways to the beta-chain and gamma-chain binding pockets.

Literature references that cite this PDB file's key reference

  PubMed id Reference
17090548 A.A.Amelot, M.Tagzirt, G.Ducouret, R.L.Kuen, and B.F.Le Bonniec (2007).
Platelet factor 4 (CXCL4) seals blood clots by altering the structure of fibrin.
  J Biol Chem, 282, 710-720.  
16999847 R.Asselta, S.Duga, and M.L.Tenchini (2006).
The molecular basis of quantitative fibrinogen disorders.
  J Thromb Haemost, 4, 2115-2129.  
15893663 N.Rai, M.Nöllmann, B.Spotorno, G.Tassara, O.Byron, and M.Rocco (2005).
SOMO (SOlution MOdeler) differences between X-Ray- and NMR-derived bead models suggest a role for side chain flexibility in protein hydrodynamics.
  Structure, 13, 723-734.  
15998829 R.I.Litvinov, O.V.Gorkun, S.F.Owen, H.Shuman, and J.W.Weisel (2005).
Polymerization of fibrin: specificity, strength, and stability of knob-hole interactions studied at the single-molecule level.
  Blood, 106, 2944-2951.  
15099268 R.F.Doolittle (2004).
Determining the crystal structure of fibrinogen.
  J Thromb Haemost, 2, 683-689.  
12871284 C.J.Davidson, E.G.Tuddenham, and J.H.McVey (2003).
450 million years of hemostasis.
  J Thromb Haemost, 1, 1487-1494.  
12871291 R.F.Doolittle (2003).
X-ray crystallographic studies on fibrinogen and fibrin.
  J Thromb Haemost, 1, 1559-1565.  
12490209 R.F.Doolittle (2003).
Structural basis of the fibrinogen-fibrin transformation: contributions from X-ray crystallography.
  Blood Rev, 17, 33-41.  
12808152 Y.Jiang, and R.F.Doolittle (2003).
The evolution of vertebrate blood coagulation as viewed from a comparison of puffer fish and sea squirt genomes.
  Proc Natl Acad Sci U S A, 100, 7527-7532.  
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.