MolNFT v1 · #126411 · protein
Structure of cobinamide-bound btuf, the periplasmic vitamin B12 binding protein in E.COLI
5M29 · Vitamin B12-binding protein: “Structure of cobinamide-bound btuf, the periplasmic vitamin B12 binding protein in E.COLI”. X-ray diffraction, 2 ligands (CBY, CYN), 6 pockets (best druggability 0.75). MolNFT v1 #126411 on GenesisL1…
- PDB
- 5M29
- Type
- protein
- Length
- 458 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vitamin B12-binding protein
- UniProt
- P37028
- Ligands
- CBY, CYN
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Vitamin B12-binding protein | protein | 229 | 41% helix, 17% strand | P37028 |
Ligands and binding sites
- CBY · Cob(ii)inamide · ligand · 2 copies · chains A, B
- CYN · Cyanide ion · ion · 3 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 180 | 0.75 | 0.91 | 30 | GOL |
| 2 | 1071 | 0.74 | 0.77 | 78 | CBY, CYN |
| 3 | 96 | 0.37 | 0.75 | 15 | empty |
| 4 | 65 | 0.31 | 0.75 | 12 | empty |
| 5 | 61 | 0.30 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1140 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5M29 · Structure of cobinamide-bound BtuF, the periplasmic vitamin B12 binding protein in E.coli · the same entry in another collection · chain A against A, TM-score 1.00
- P37028 · AlphaFold monomer V2.0 prediction for vitamin B12-binding protein (P37028) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P37028
- Elsewhere: RCSB PDB 5M29 · PDBe 5M29 · UniProt P37028
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.