Research workbench
Crystal structure of the phosphorolytic exoribonuclease RNase pH from bacillus subtilis
Analyse Crystal structure of the phosphorolytic exoribonuclease RNase pH from bacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1OYP
- Type
- protein
- Length
- 1,356 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease pH
- EC
- 2.7.7.56
- UniProt
- P28619
- Ligands
- SO4
- Pockets
- 11 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Ribonuclease pH (EC 2.7.7.56) | protein | 226 | 34% helix, 31% strand | P28619 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 12 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 359 | 0.63 | 0.79 | 37 | SO4 |
| 2 | 309 | 0.63 | 0.80 | 41 | empty |
| 3 | 356 | 0.63 | 0.79 | 44 | SO4 |
| 4 | 342 | 0.62 | 0.79 | 39 | SO4 |
| 5 | 381 | 0.61 | 0.77 | 39 | SO4 |
Interfaces
6 interfaces between chains.
- A–B · 1389 Ų buried · 29 hydrogen bonds · protein-protein
- E–F · 1348 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1269 Ų buried · 19 hydrogen bonds · protein-protein
- D–E · 462 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 449 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 1OYP · Crystal Structure of the phosphorolytic exoribonuclease RNase PH from Bacillus subtilis · the same entry in another collection · chain C against C, TM-score 1.00
- P28619 · AlphaFold monomer V2.0 prediction for ribonuclease pH (P28619) · 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 P28619
- Elsewhere: RCSB PDB 1OYP · PDBe 1OYP · UniProt P28619
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