Research workbench
Structural genomics, 2.2A crystal structure of protein ykof from bacillus subtilis
Analyse Structural genomics, 2.2A crystal structure of protein ykof from bacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1S7H
- Type
- protein
- Length
- 732 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ykof
- UniProt
- O34911
- Pockets
- 9 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ykof | protein | 186 | 34% helix, 29% strand | O34911 |
| B | Ykof | protein | 180 | 36% helix, 30% strand | O34911 |
| C | Ykof | protein | 182 | 34% helix, 30% strand | O34911 |
| D | Ykof | protein | 184 | 34% helix, 29% strand | O34911 |
Pockets
9 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 113 | 0.77 | 0.97 | 32 | empty |
| 2 | 304 | 0.75 | 0.87 | 54 | empty |
| 3 | 181 | 0.58 | 0.81 | 25 | empty |
| 4 | 164 | 0.58 | 0.82 | 26 | empty |
| 5 | 186 | 0.58 | 0.81 | 27 | empty |
Interfaces
2 interfaces between chains.
- A–B · 2166 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 2123 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 1S7H · Structural Genomics, 2.2A crystal structure of protein YKOF from Bacillus subtilis · the same entry in another collection · chain C against C, 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 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 1S7H · PDBe 1S7H · UniProt O34911
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