› 6ndc

X-ray diffraction
3.35Å resolution

RHODOCETIN IN COMPLEX WITH THE INTEGRIN ALPHA2-A DOMAIN WITH CHROMIUM BOUND

Released:
DOI: 10.2210/pdb6ndc/pdb
PDB 6ndc coloured by chain and viewed from the front.
PDB 6ndc coloured by chain and viewed from the side.
PDB 6ndc coloured by chain and viewed from the top.
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:
Non-polymer only trimer (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
Molecule details ›
Chains: C, F, I, L, O, R
Length: 217 amino acids
Theoretical weight: 23.74 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P17301 (Residues: 170-366; Coverage: 17%)
Gene names: CD49B, ITGA2
Sequence domains: von Willebrand factor type A domain
Structure domains: von Willebrand factor, type A domain

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU
Spacegroup: P41
Unit cell:
a: 131.14Å b: 131.14Å c: 251.46Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.218 0.215 0.276
Expression system: Escherichia coli

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