Research workbench
Crystal structure of RNase III from aquifex aeolicus complexed with ds-RNA at 2.5-ångström resolution
Analyse Crystal structure of RNase III from aquifex aeolicus complexed with ds-RNA at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2NUF
- Type
- protein + RNA
- Length
- 494 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 28-mer; Ribonuclease III
- EC
- 3.1.26.3
- UniProt
- O67082
- Ligands
- MG
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 60% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | 28-mer | rna | 28 | — | — |
| A, B | Ribonuclease III (EC 3.1.26.3) | protein | 219 | 60% helix, 11% strand | O67082 |
Ligands and binding sites
- MG · Magnesium ion · metal · 8 copies · chains C, D, B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 682 | 0.83 | 0.87 | 69 | MG |
| 2 | 142 | 0.54 | 0.82 | 24 | empty |
| 3 | 102 | 0.50 | 0.83 | 20 | MG |
| 4 | 81 | 0.43 | 0.81 | 10 | empty |
| 5 | 75 | 0.33 | 0.75 | 13 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1153 Ų buried · 18 hydrogen bonds · protein-protein
- D–B · 691 Ų buried · 11 hydrogen bonds · protein-nucleic
- C–A · 687 Ų buried · 10 hydrogen bonds · protein-nucleic
- C–B · 681 Ų buried · 20 hydrogen bonds · protein-nucleic
- D–A · 679 Ų buried · 26 hydrogen bonds · protein-nucleic
Compared structures
- 2NUF · Crystal structure of RNase III from Aquifex aeolicus complexed with ds-RNA at… · the same entry in another collection · chain C against C, TM-score 1.00
- O67082 · AlphaFold monomer V2.0 prediction for ribonuclease 3 (O67082) · a predicted model of the same protein · chain A against A, TM-score 0.85
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 O67082
- Elsewhere: RCSB PDB 2NUF · PDBe 2NUF · UniProt O67082
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