MolNFT v1 · #15379 · protein
2.0 ångström structure of btuf, the vitamin B12 binding protein of E. COLI
1N2Z · Vitamin B12 transport protein btuf: “2.0 ångström structure of btuf, the vitamin B12 binding protein of E. COLI”. X-ray diffraction, 3 ligands (CNC, CD, CL), 4 pockets (best druggability 0.73). MolNFT v1 #15379 on GenesisL1: 3D…
- 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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