MolNFT v1 · #21405 · protein
The structure and function of B. subtilis ykof gene product: ligand free protein
1S99: “The structure and function of B. subtilis ykof gene product: ligand free protein”. X-ray diffraction, 1 ligand (CA), 5 pockets (best druggability 0.79). MolNFT v1 #21405 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1S99
- Type
- protein
- Length
- 366 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ykof
- UniProt
- O34911
- Ligands
- CA
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ykof | protein | 186 | 32% helix, 29% strand | O34911 |
| B | Ykof | protein | 180 | 33% helix, 30% strand | O34911 |
Ligands and binding sites
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 | 126 | 0.79 | 0.97 | 33 | empty |
| 2 | 161 | 0.60 | 0.83 | 24 | ACT |
| 3 | 212 | 0.59 | 0.80 | 27 | empty |
| 4 | 198 | 0.59 | 0.81 | 27 | empty |
| 5 | 139 | 0.56 | 0.82 | 22 | ACT |
Interfaces
1 interface between chains.
- A–B · 2145 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
- 1S99 · The structure and function of B. subtilis YkoF gene product: ligand free protein · 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 B 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 O34911
- Elsewhere: RCSB PDB 1S99 · PDBe 1S99 · UniProt O34911
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