› 3gpr

X-ray diffraction
3.2Å resolution

Crystal structure of rhodocetin

Released:
DOI: 10.2210/pdb3gpr/pdb
PDB entry 3gpr coloured by chain, front view.
PDB entry 3gpr coloured by chain, side view.
PDB entry 3gpr coloured by chain, top view.
Source organism: Calloselasma rhodostoma
Primary publication:
The alpha2beta1 integrin-specific antagonist rhodocetin is a cruciform, heterotetrameric molecule.
Eble JA, Niland S, Bracht T, Mormann M, Peter-Katalinic J, Pohlentz G, Stetefeld J
FASEB J 23 2917-27 (2009)
PMID: 19369383

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-112443 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Snaclec rhodocetin subunit alpha Chain: A
Molecule details ›
Chain: A
Length: 133 amino acids
Theoretical weight: 15.98 KDa
Source organism: Calloselasma rhodostoma
UniProt:
  • Canonical: P81397 (Residues: 1-133; Coverage: 100%)
Sequence domains: Lectin C-type domain
Structure domains: Mannose-Binding Protein A, subunit A
Snaclec rhodocetin subunit beta Chain: B
Molecule details ›
Chain: B
Length: 129 amino acids
Theoretical weight: 15.21 KDa
Source organism: Calloselasma rhodostoma
UniProt:
  • Canonical: P81398 (Residues: 1-129; Coverage: 100%)
Sequence domains: Lectin C-type domain
Structure domains: Mannose-Binding Protein A, subunit A
Snaclec rhodocetin subunit gamma Chain: C
Molecule details ›
Chain: C
Length: 134 amino acids
Theoretical weight: 15.62 KDa
Source organism: Calloselasma rhodostoma
UniProt:
  • Canonical: D2YW39 (Residues: 2-135; Coverage: 99%)
Sequence domains: Lectin C-type domain
Structure domains: Mannose-Binding Protein A, subunit A
Snaclec rhodocetin subunit delta Chain: D
Molecule details ›
Chain: D
Length: 124 amino acids
Theoretical weight: 14.74 KDa
Source organism: Calloselasma rhodostoma
UniProt:
  • Canonical: D2YW40 (Residues: 1-124; Coverage: 100%)
Sequence domains: Lectin C-type domain
Structure domains: Mannose-Binding Protein A, subunit A

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA
Spacegroup: P65
Unit cell:
a: 83.546Å b: 83.546Å c: 196.078Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.223 0.223 0.284

Quick links

Citations

5 review citations

C-type lectin-like proteins from snake venoms.
Arlinghaus et al. (2012)
4 more

2 mentions without citation

Dramatic and concerted conformational changes enable rhodocetin to block α2β1 integrin selectively.
Eble et al. (2017)
1 more