MolNFT v1 · #102523 · protein + RNA
Crystal structure of yeast RNase III (RNT1P) complexed with the product of dsrna processing
4OOG · Ribonuclease 3: “Crystal structure of yeast RNase III (RNT1P) complexed with the product of dsrna processing”. X-ray diffraction, 1 ligand (MG), 4 pockets (best druggability 0.61). MolNFT v1 #102523 on GenesisL1: 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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