PDBsum entry: 1lwu

Blood clotting

PDB id: 1lwu

Contents

Protein chains

99 a.a. *

315 a.a. *

317 a.a. *

Ligands

GLY-HIS-ARG-PRO ×4

NH2 ×4

NDG ×8

MAN ×8

NAG ×4

BMA ×3

GAL

NAG-NAG-MAN

NAG-NAG ×2

Metals

_CA ×8

* Residue conservation analysis

PDB id:

1lwu

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)

Resolution:

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

Date:

03-Jun-02 Release date: 23-Aug-02

Protein chains

P02674  (FIBA1_PETMA) -  Fibrinogen alpha-1 chain (Fragment)

Seq: 966 a.a.

Struc: 99 a.a.*

Protein chains

P02678  (FIBB_PETMA) -  Fibrinogen beta chain (Fragments)

Seq: 477 a.a.

Struc: 315 a.a.

Protein chains

P04115  (FIBG_PETMA) -  Fibrinogen gamma chain

Seq: 432 a.a.

Struc: 317 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 

• Cellular component: extracellular space (2 terms)
• 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.

ABSTRACT

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.