› 1n86

X-ray diffraction
3.2Å resolution

Crystal structure of human D-dimer from cross-linked fibrin complexed with GPR and GHRPLDK peptide ligands.

Released:
DOI: 10.2210/pdb1n86/pdb
PDB entry 1n86 coloured by chain, front view.
PDB entry 1n86 coloured by chain, side view.
PDB entry 1n86 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
The crystal structure of fragment double-D from cross-linked lamprey fibrin reveals isopeptide linkages across an unexpected D-D interface.
Yang Z, Pandi L, Doolittle RF
Biochemistry 41 15610-7 (2002)
PMID: 12501189

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero decamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-136020 (preferred)
Entry contents:
5 distinct polypeptide molecules
Macromolecules (5 distinct):
Fibrinogen alpha chain Chains: A, D
Molecule details ›
Chains: A, D
Length: 87 amino acids
Theoretical weight: 10.24 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P02671 (Residues: 130-216; Coverage: 10%)
Gene name: FGA
Sequence domains: Fibrinogen alpha/beta chain family
Structure domains: Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Fibrinogen beta chain Chains: B, E
Molecule details ›
Chains: B, E
Length: 328 amino acids
Theoretical weight: 37.69 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P02675 (Residues: 164-491; Coverage: 71%)
Gene name: FGB
Sequence domains:
Structure domains:
Fibrinogen gamma chain Chains: C, F
Molecule details ›
Chains: C, F
Length: 324 amino acids
Theoretical weight: 36.69 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P02679 (Residues: 114-433; Coverage: 75%)
Gene names: FGG, PRO2061
Sequence domains:
Structure domains:
Fibrinogen alpha chain Chains: G, H
Molecule details ›
Chains: G, H
Length: 3 amino acids
Theoretical weight: 329 Da
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P02671 (Residues: 36-38; Coverage: 0%)
Gene name: FGA
Fibrinogen beta chain Chains: I, J
Molecule details ›
Chains: I, J
Length: 7 amino acids
Theoretical weight: 825 Da
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P02675 (Residues: 45-51; Coverage: 2%)
Gene name: FGB

Ligands and Environments

3 bound ligands:
Ligand NDG 4 x NDG
Ligand MAN 1 x MAN
Ligand CA 4 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU
Spacegroup: P212121
Unit cell:
a: 52.328Å b: 130.093Å c: 298.313Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.23 0.226 0.289
Expression system: Not provided

Quick links

Citations

4 review citations

Breaking symmetry in protein dimers: designs and functions.
Brown JH. (2006)
3 more

3 mentions without citation

Atomic Structural Models of Fibrin Oligomers.
Zhmurov et al. (2018)
2 more