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The ligand-free structure of E COLI btuf, the periplasmic binding protein for vitamin B12
Analyse The ligand-free structure of E COLI btuf, the periplasmic binding protein for… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1N4D
- Type
- protein
- Length
- 471 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vitamin B12 transport protein btuf
- UniProt
- P37028
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vitamin B12 transport protein btuf | protein | 244 | 42% helix, 11% strand | P37028 |
| B | Vitamin B12 transport protein btuf | protein | 227 | 40% helix, 12% strand | P37028 |
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 | 413 | 0.65 | 0.78 | 49 | empty |
| 2 | 363 | 0.59 | 0.76 | 42 | empty |
| 3 | 78 | 0.33 | 0.74 | 15 | empty |
| 4 | 65 | 0.32 | 0.75 | 13 | empty |
Modifications
Observed in the structure: 4 modified, 1 disulfide (engineered, disulfide).
Compared structures
- 1N4D · The Ligand-Free Structure of E coli BtuF, the Periplasmic Binding Protein for Vitamin B12 · 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 0.96
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 1N4D · PDBe 1N4D · UniProt P37028
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