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Structure of cobinamide-bound btuf mutant W66Y, the periplasmic vitamin B12 binding protein in E.COLI
Analyse Structure of cobinamide-bound btuf mutant W66Y, the periplasmic vitamin B12… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5M34
- Type
- protein
- Length
- 457 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 0.77
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vitamin B12-binding protein | protein | 228 | 40% helix, 16% strand | P37028 |
| B | Vitamin B12-binding protein | protein | 229 | 39% helix, 16% 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 · 2 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 | 181 | 0.77 | 0.92 | 29 | empty |
| 2 | 929 | 0.76 | 0.79 | 77 | CBY, CYN, GOL |
| 3 | 83 | 0.35 | 0.75 | 13 | empty |
| 4 | 65 | 0.32 | 0.76 | 17 | empty |
| 5 | 64 | 0.30 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1230 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5M34 · Structure of cobinamide-bound BtuF mutant W66Y, the periplasmic vitamin B12 binding… · 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 0.97
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 5M34 · PDBe 5M34 · UniProt P37028
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