MolNFT v1 · #16157 · protein
Outer membrane cobalamin transporter (btub) from E. COLI, with bound calcium and cyanocobalamin (vitamin B12) substrate
1NQH · Vitamin B12 receptor: “Outer membrane cobalamin transporter (btub) from E. COLI, with bound calcium and cyanocobalamin (vitamin B12)…”. X-ray diffraction, 2 ligands (CNC, CA), 9 pockets (best druggability 0.87). MolNFT v1 #16157 on…
- PDB
- 1NQH
- Type
- protein
- Length
- 584 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vitamin B12 receptor
- UniProt
- P06129
- Ligands
- CNC, CA
- Pockets
- 9 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vitamin B12 receptor | protein | 584 | 6% helix, 57% strand | P06129 |
Ligands and binding sites
- CNC · Cyanocobalamin · ligand · chains A
- CA · Calcium ion · metal · 4 copies · chains A
- C8E · (hydroxyethyloxy)tri(ethyloxy)octane · additive · 6 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 897 | 0.87 | 0.89 | 122 | empty |
| 2 | 183 | 0.78 | 0.94 | 33 | empty |
| 3 | 65 | 0.72 | 0.98 | 26 | empty |
| 4 | 666 | 0.71 | 0.79 | 83 | CNC |
| 5 | 505 | 0.69 | 0.80 | 50 | empty |
Compared structures
- 1NQH · Outer membrane cobalamin transporter (btub) from E. COLI, with bound calcium and… · the same entry in another collection · chain A against A, TM-score 1.00
- P06129 · AlphaFold monomer V2.0 prediction for vitamin B12 transporter btub (P06129) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P06129
- Elsewhere: RCSB PDB 1NQH · PDBe 1NQH · UniProt P06129
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