Research workbench
Outer membrane cobalamin transporter (btub) from E. COLI, with bound calcium and cyanocobalamin (vitamin B12) substrate
Analyse Outer membrane cobalamin transporter (btub) from E. COLI, with bound calcium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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