Research workbench
Crystal structure of yeast RNase III (RNT1P) complexed with the product of dsrna processing
Analyse Crystal structure of yeast RNase III (RNT1P) complexed with the product of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OOG
- Type
- protein + RNA
- Length
- 514 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease 3; 34-mer RNA
- EC
- 3.1.26.3
- UniProt
- Q02555
- Ligands
- MG
- Pockets
- 4 · best druggability 0.61
Structure
x-ray diffraction · 4 distinct chains · 63% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonuclease 3 | protein | 109 | 70% helix, 0% strand | Q02555 |
| B | Ribonuclease 3 | protein | 110 | 68% helix, 0% strand | Q02555 |
| C | Ribonuclease 3 (EC 3.1.26.3) | protein | 261 | 57% helix, 8% strand | Q02555 |
| D | 34-mer RNA | rna | 34 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 271 | 0.61 | 0.80 | 24 | empty |
| 2 | 509 | 0.58 | 0.74 | 27 | MG |
| 3 | 339 | 0.57 | 0.76 | 34 | empty |
| 4 | 111 | 0.40 | 0.76 | 19 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3578 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1552 Ų buried · 39 hydrogen bonds · protein-nucleic
- A–C · 300 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 163 Ų buried · 1 hydrogen bond · protein-nucleic
- B–C · 121 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4OOG · Crystal structure of yeast RNase III (Rnt1p) complexed with the product of dsRNA… · the same entry in another collection · chain A against A, TM-score 1.00
- Q02555 · AlphaFold monomer V2.0 prediction for ribonuclease 3 (Q02555) · a predicted model of the same protein · chain C 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 Q02555
- Elsewhere: RCSB PDB 4OOG · PDBe 4OOG · UniProt Q02555
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