› 1lwu

X-ray diffraction
2.8Å resolution

Crystal structure of fragment D from lamprey fibrinogen complexed with the peptide Gly-His-Arg-Pro-amide

Released:
DOI: 10.2210/pdb1lwu/pdb
PDB 1lwu coloured by chain and viewed from the front.
PDB 1lwu coloured by chain and viewed from the side.
PDB 1lwu coloured by chain and viewed from the top.
Source organism: Petromyzon marinus
Primary publication:
Crystal structure of fragment D from lamprey fibrinogen complexed with the peptide Gly-His-Arg-Pro-amide.
Yang Z, Spraggon G, Pandi L, Everse SJ, Riley M, Doolittle RF
Biochemistry 41 10218-24 (2002)
PMID: 12162736

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
hetero octamer (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (5 distinct):
Fibrinogen alpha-1 chain Chains: A, D, G, J
Molecule details ›
Chains: A, D, G, J
Length: 119 amino acids
Theoretical weight: 14.07 KDa
Source organism: Petromyzon marinus
UniProt:
  • Canonical: P02674 (Residues: 87-205; Coverage: 12%)
Structure domains: Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Fibrinogen beta chain Chains: B, E, H, K
Molecule details ›
Chains: B, E, H, K
Length: 323 amino acids
Theoretical weight: 37.06 KDa
Source organism: Petromyzon marinus
UniProt:
  • Canonical: P02678 (Residues: 155-477; Coverage: 68%)
Structure domains:
Fibrinogen gamma chain Chains: C, F, I, L
Molecule details ›
Chains: C, F, I, L
Length: 323 amino acids
Theoretical weight: 37.48 KDa
Source organism: Petromyzon marinus
UniProt:
  • Canonical: P04115 (Residues: 103-425; Coverage: 79%)
Gene name: FGG
Sequence domains: Fibrinogen beta and gamma chains, C-terminal globular domain
Structure domains:
Ligand Gly-His-Arg-Pro-NH2 Chains: M, N, O, P
Molecule details ›
Chains: M, N, O, P
Length: 5 amino acids
Theoretical weight: 466 Da

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Ligand NAG 2 x NAG
7 bound ligands:
Ligand NDG 8 x NDG
Ligand MAN 9 x MAN
Ligand CA 8 x CA
Ligand NAG 8 x NAG
Ligand BMA 3 x BMA
Ligand GAL 1 x GAL
Ligand NH2 4 x NH2
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X12C
Spacegroup: P1
Unit cell:
a: 76.735Å b: 47.654Å c: 244.65Å
α: 88.81° β: 97.23° γ: 86.17°
R-values:
R R work R free
0.251 0.245 0.287

Quick links

Citations

4 review citations

The molecular basis of quantitative fibrinogen disorders.
Asselta et al. (2006)
3 more

1 mention without citation

Rare Variant Analysis of Human and Rodent Obesity Genes in Individuals with Severe Childhood Obesity.
Hendricks et al. (2017)