Research workbench
2.0 ångström structure of btuf, the vitamin B12 binding protein of E. COLI
Analyse 2.0 ångström structure of btuf, the vitamin B12 binding protein of E. COLI in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1N2Z
- Type
- protein
- Length
- 490 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vitamin B12 transport protein btuf
- UniProt
- P37028
- Ligands
- CNC, CD, CL
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Vitamin B12 transport protein btuf | protein | 245 | 44% helix, 16% strand | P37028 |
Ligands and binding sites
- CNC · Cyanocobalamin · ligand · 2 copies · chains A, B
- CD · Cadmium ion · metal · 22 copies · chains A, B
- CL · Chloride ion · ion · 6 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 195 | 0.73 | 0.89 | 30 | CD, PG4 |
| 2 | 908 | 0.71 | 0.76 | 81 | CD, CL, CNC |
| 3 | 169 | 0.48 | 0.77 | 21 | empty |
| 4 | 140 | 0.40 | 0.74 | 17 | CD |
Interfaces
1 interface between chains.
- A–B · 1037 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 1N2Z · 2.0 Angstrom structure of BtuF, the vitamin B12 binding protein of 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 1N2Z · PDBe 1N2Z · UniProt P37028
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