› 6x8z

X-ray diffraction
2.5Å resolution

Crystal structure of N-truncated human B12 chaperone CblD(C262S)-thiolato-cob(III)alamin complex (108-296)

Released:
DOI: 10.2210/pdb6x8z/pdb
PDB entry 6x8z coloured by chain, front view.
PDB entry 6x8z coloured by chain, side view.
PDB entry 6x8z coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
An Interprotein Co-S Coordination Complex in the B12-Trafficking Pathway.
Li Z, Mascarenhas R, Twahir UT, Kallon A, Deb A, Yaw M, Penner-Hahn J, Koutmos M, Warncke K, Banerjee R
J Am Chem Soc 142 16334-16345 (2020)
PMID: 32871076

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
Cellular component:
  • not assigned
Sequence domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-190579 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Cobalamin trafficking protein CblD Chains: A, B
Molecule details ›
Chains: A, B
Length: 192 amino acids
Theoretical weight: 21.82 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9H3L0 (Residues: 108-296; Coverage: 64%)
Gene names: C2orf25, CL25022, HSPC161, MMADHC, My011
Sequence domains: Methylmalonic aciduria and homocystinuria type D protein

Ligands and Environments

1 bound ligand:
Ligand B12 2 x B12
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-G
Spacegroup: C2
Unit cell:
a: 103.222Å b: 69.776Å c: 64.266Å
α: 90° β: 101.15° γ: 90°
R-values:
R R work R free
0.251 0.249 0.279
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Versatile enzymology and heterogeneous phenotypes in cobalamin complementation type C disease.
Esser et al. (2022)
1 more

2 mentions without citation

Redox-Linked Coordination Chemistry Directs Vitamin B12 Trafficking.
Banerjee et al. (2021)
1 more