MolNFT v1 · #169343 · protein
Crystal structure of N-truncated human B12 chaperone CBLD(C262S)- thiolato-COB(III)ALAMIN complex (108-296)
6X8Z · Methylmalonic aciduria and homocystinuria type D protein…: “Crystal structure of N-truncated human B12 chaperone CBLD(C262S)- thiolato-COB(III)ALAMIN complex (108-296)”. X-ray diffraction, 1 ligand (B12), 3 pockets (best…
- PDB
- 6X8Z
- Type
- protein
- Length
- 308 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methylmalonic aciduria and homocystinuria type D protein, mitochondrial
- EC
- 1.-.-.-
- UniProt
- Q9H3L0
- Ligands
- B12
- Pockets
- 3 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methylmalonic aciduria and homocystinuria type D protein, mitochondrial (EC 1.-.-.-) | protein | 158 | 32% helix, 25% strand | Q9H3L0 |
| B | Methylmalonic aciduria and homocystinuria type D protein, mitochondrial (EC 1.-.-.-) | protein | 150 | 35% helix, 27% strand | Q9H3L0 |
Ligands and binding sites
- B12 · Cobalamin · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 221 | 0.57 | 0.79 | 27 | empty |
| 2 | 184 | 0.57 | 0.80 | 27 | empty |
| 3 | 274 | 0.53 | 0.75 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 991 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6X8Z · Crystal structure of N-truncated human B12 chaperone CblD(C262S)-thiolato-cob(III)alamin… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9H3L0 · AlphaFold monomer V2.0 prediction for cobalamin trafficking protein cbld (Q9H3L0) · a predicted model of the same protein · chain B against A, TM-score 0.94
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q9H3L0
- Elsewhere: RCSB PDB 6X8Z · PDBe 6X8Z · UniProt Q9H3L0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.