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
- 1OYR
- Type
- protein
- Length
- 1,452 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
- CD, SO4
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Ribonuclease pH (EC 2.7.7.56) | protein | 242 | 33% helix, 30% strand | P28619 |
Ligands and binding sites
- CD · Cadmium ion · metal · 3 copies · chains A, E, D
- 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
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 767 | 0.77 | 0.81 | 98 | SO4 |
| 2 | 1042 | 0.75 | 0.78 | 131 | SO4 |
| 3 | 640 | 0.74 | 0.81 | 83 | SO4 |
| 4 | 143 | 0.67 | 0.88 | 32 | empty |
| 5 | 156 | 0.64 | 0.86 | 32 | empty |
Interfaces
12 interfaces between chains.
- D–E · 1560 Ų buried · 26 hydrogen bonds · protein-protein
- A–F · 1466 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 1401 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 1398 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 1346 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 1OYR · 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 1OYR · PDBe 1OYR · UniProt P28619
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