Research workbench
Outer membrane cobalamin transporter (btub) from E. COLI, with bound calcium
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
- 1NQG
- Type
- protein
- Length
- 576 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vitamin B12 receptor
- UniProt
- P06129
- Ligands
- CA
- Pockets
- 6 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 58% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vitamin B12 receptor | protein | 576 | 6% helix, 58% strand | P06129 |
Ligands and binding sites
- 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
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1102 | 0.88 | 0.89 | 134 | empty |
| 2 | 148 | 0.79 | 0.96 | 45 | empty |
| 3 | 77 | 0.74 | 0.98 | 32 | empty |
| 4 | 503 | 0.68 | 0.79 | 47 | empty |
| 5 | 588 | 0.65 | 0.76 | 76 | empty |
Compared structures
- 1NQG · Outer membrane cobalamin transporter (btub) from E. COLI, with bound calcium · 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 1NQG · PDBe 1NQG · UniProt P06129
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