› 2z4e

X-ray diffraction
2.7Å resolution

Crystal Structure of D-Dimer from Human Fibrin Complexed with Gly-His-Arg-Pro-Tyr-amide

Released:
DOI: 10.2210/pdb2z4e/pdb
PDB entry 2z4e coloured by chain, front view.
PDB entry 2z4e coloured by chain, side view.
PDB entry 2z4e coloured by chain, top view.
Source organisms:
Primary publication:
Probing the beta-chain hole of fibrinogen with synthetic peptides that differ at their amino termini.
Doolittle RF, Pandi L
Biochemistry 46 10033-8 (2007)
PMID: 17688324

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
hetero decamer (preferred)
hetero pentamer
Assembly name:
PDBe Complex ID:
PDB-CPX-136023 (preferred)
Entry contents:
5 distinct polypeptide molecules
Macromolecules (6 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: 326 amino acids
Theoretical weight: 37.44 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P02675 (Residues: 164-489; 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:
Fibrin B knob (tetrapeptide) Chains: S, T
Molecule details ›
Chains: S, T
Length: 4 amino acids
Theoretical weight: 468 Da
Fibrinogen beta chain Chains: I, J
Molecule details ›
Chains: I, J
Length: 5 amino acids
Theoretical weight: 631 Da
Source organism: Bos taurus
Expression system: Not provided
UniProt:
  • Canonical: P02676 (Residues: 22-26; Coverage: 1%)
Gene name: FGB

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
2 bound ligands:
Ligand CA 8 x CA
Ligand NAG 2 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.1
Spacegroup: P212121
Unit cell:
a: 54.63Å b: 148.69Å c: 232.68Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.22 0.216 0.275
Expression system: Not provided

Quick links

Citations

2 review citations

D-dimer antigen: current concepts and future prospects.
Adam et al. (2009)
1 more

2 mentions without citation

Structural effects of methionine oxidation on isolated subdomains of human fibrin D and αC regions.
Burney et al. (2014)
1 more