MolNFT v1 · #21478 · protein
The structure and function of B. subtilis ykof gene product: the complex with thiamin
1SBR: “The structure and function of B. subtilis ykof gene product: the complex with thiamin”. X-ray diffraction, 2 ligands (VIB, CA), 5 pockets (best druggability 0.78). MolNFT v1 #21478 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1SBR
- Type
- protein
- Length
- 364 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ykof
- UniProt
- O34911
- Ligands
- VIB, CA
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ykof | protein | 182 | 32% helix, 31% strand | O34911 |
| B | Ykof | protein | 182 | 35% helix, 30% strand | O34911 |
Ligands and binding sites
- VIB · 3-(4-amino-2-methyl-pyrimidin-5-ylmethyl)-5-(2-hydroxy-ethyl)-4-methyl-thiazol-3-ium · ligand · 4 copies · chains A, B
- CA · Calcium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 119 | 0.78 | 0.98 | 35 | empty |
| 2 | 236 | 0.62 | 0.81 | 27 | VIB |
| 3 | 255 | 0.61 | 0.80 | 29 | VIB |
| 4 | 137 | 0.60 | 0.84 | 24 | VIB |
| 5 | 132 | 0.54 | 0.81 | 22 | VIB |
Interfaces
1 interface between chains.
- A–B · 2097 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
- 1SBR · The structure and function of B. subtilis YkoF gene product: the complex with thiamin · the same entry in another collection · chain A against A, TM-score 1.00
- O34911 · AlphaFold monomer V2.0 prediction for putative HMP/THIAMINE-binding protein ykof (O34911) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 O34911
- Elsewhere: RCSB PDB 1SBR · PDBe 1SBR · UniProt O34911
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