Research workbench
Crystal structure of the purine operon repressor of bacillus subtilis
Analyse Crystal structure of the purine operon repressor of bacillus subtilis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1O57
- Type
- protein
- Length
- 1,078 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pur operon repressor
- UniProt
- P37551
- Ligands
- SO4
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Pur operon repressor | protein | 270 | 37% helix, 27% strand | P37551 |
| B, C | Pur operon repressor | protein | 269 | 38% helix, 29% strand | P37551 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A, B, C, D
- P6G · Hexaethylene glycol · additive · 2 copies · chains A, D
- 1PE · Pentaethylene glycol · additive · 2 copies · chains C, D
- 2PE · Nonaethylene glycol · additive · chains A, B
- PG4 · Tetraethylene glycol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 823 | 0.81 | 0.84 | 66 | 1PE |
| 2 | 843 | 0.81 | 0.83 | 65 | 2PE, PG4 |
| 3 | 509 | 0.72 | 0.81 | 58 | SO4 |
| 4 | 448 | 0.69 | 0.80 | 56 | SO4 |
| 5 | 248 | 0.62 | 0.81 | 31 | SO4, EPE |
Interfaces
3 interfaces between chains.
- C–D · 1628 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1615 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 405 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1O57 · Crystal structure of the purine operon repressor of bacillus subtilis · the same entry in another collection · chain A against A, TM-score 1.00
- P37551 · AlphaFold monomer V2.0 prediction for pur operon repressor (P37551) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P37551
- Elsewhere: RCSB PDB 1O57 · PDBe 1O57 · UniProt P37551
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