MolNFT v1 · #115819 · protein
Crystal structure of N-terminal truncated human B12-chaperone cbld (108-296)
5CV0 · Methylmalonic aciduria and homocystinuria type D protein…: “Crystal structure of N-terminal truncated human B12-chaperone cbld (108-296)”. X-ray diffraction, 3 pockets (best druggability 0.64). MolNFT v1 #115819 on GenesisL1: 3D…
- PDB
- 5CV0
- Type
- protein
- Length
- 332 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methylmalonic aciduria and homocystinuria type D protein, mitochondrial
- UniProt
- Q9H3L0
- Pockets
- 3 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methylmalonic aciduria and homocystinuria type D protein, mitochondrial | protein | 170 | 29% helix, 24% strand | Q9H3L0 |
| B | Methylmalonic aciduria and homocystinuria type D protein, mitochondrial | protein | 162 | 31% helix, 25% strand | Q9H3L0 |
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 503 | 0.64 | 0.77 | 33 | empty |
| 2 | 89 | 0.56 | 0.86 | 23 | empty |
| 3 | 75 | 0.41 | 0.79 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1515 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 5CV0 · Crystal structure of N-terminal truncated human B12-chaperone CblD (108-296) · the same entry in another collection · chain B against B, 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 5CV0 · PDBe 5CV0 · UniProt Q9H3L0
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