Research workbench
Crystal structure of periplasmic vitamin B12 binding protein btuf of vibrio cholerae
Analyse Crystal structure of periplasmic vitamin B12 binding protein btuf of vibrio… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YSC
- Type
- protein
- Length
- 255 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vitamin B12-binding protein
- UniProt
- A5F5P5
- Ligands
- CNC, SO4
- Pockets
- 1 · best druggability 0.56
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vitamin B12-binding protein | protein | 255 | 44% helix, 14% strand | A5F5P5 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 292 | 0.56 | 0.76 | 38 | CNC |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5YSC · Crystal Structure of periplasmic Vitamin B12 binding protein BtuF of Vibrio cholerae · the same entry in another collection · chain A against A, TM-score 1.00
- A5F5P5 · AlphaFold monomer V2.0 prediction for vitamin B12-binding protein (A5F5P5) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 A5F5P5
- Elsewhere: RCSB PDB 5YSC · PDBe 5YSC · UniProt A5F5P5
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