› 6ndh

X-ray diffraction
2.9Å resolution

RHODOCETIN IN COMPLEX WITH THE INTEGRIN ALPHA2-A DOMAIN AND ZINC

Released:
DOI: 10.2210/pdb6ndh/pdb
Model geometry
Fit model/data
PDB entry 6ndh coloured by chain, front view.
PDB entry 6ndh coloured by chain, side view.
PDB entry 6ndh coloured by chain, top view.
Source organisms:
Entry authors: Stetefeld J, McDougall MD, Loewen PC

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-112442 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Snaclec rhodocetin subunit gamma Chains: A, D, G, J, M, P
Molecule details ›
Chains: A, D, G, J, M, P
Length: 135 amino acids
Theoretical weight: 15.74 KDa
Source organism: Calloselasma rhodostoma
UniProt:
  • Canonical: D2YW39 (Residues: 1-135; Coverage: 100%)
Sequence domains: Lectin C-type domain
Structure domains: Mannose-Binding Protein A, subunit A
Snaclec rhodocetin subunit delta Chains: B, E, H, K, N, Q
Molecule details ›
Chains: B, E, H, K, N, Q
Length: 124 amino acids
Theoretical weight: 14.88 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
Integrin alpha-2 Chains: C, F, I, L, O, R

Ligands and Environments

5 bound ligands:
Ligand SO4 15 x SO4
Ligand ZN 6 x ZN
Ligand NA 6 x NA
Ligand CL 9 x CL
Ligand NH4 1 x NH4
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: RIGAKU
Spacegroup: P41
Unit cell:
a: 131.399Å b: 131.399Å c: 251.358Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.231 0.228 0.285
Expression system: Escherichia coli

Quick links

PDB-REDO

The sliders below show the change in model quality between original PDB entry and the PDB-REDO entry

Model Geometry
 
 
Data not available
DNA/RNA Geometry
 
 
Data not available
Fit model/data
 
 
Data not available
PDB-REDO