Research workbench
Crystal structure of RNase III from aquifex aeolicus complexed with ds-RNA at 1.7-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
- 2NUG
- Type
- protein + RNA
- Length
- 478 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(P*AP*AP*GP*GP*UP*CP*AP*UP*UP*CP*G)-3'; 5'-R(P*AP*GP*UP*GP*GP*CP*CP*UP*UP*GP*C)-3'…
- EC
- 3.1.26.3
- UniProt
- O67082
- Ligands
- MG
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 61% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | 5'-R(P*AP*AP*GP*GP*UP*CP*AP*UP*UP*CP*G)-3' | rna | 11 | — | — |
| E, F | 5'-R(P*AP*GP*UP*GP*GP*CP*CP*UP*UP*GP*C)-3' | rna | 11 | — | — |
| A | Ribonuclease III (EC 3.1.26.3) | protein | 216 | 61% helix, 12% strand | O67082 |
| B | Ribonuclease III (EC 3.1.26.3) | protein | 218 | 61% helix, 11% strand | O67082 |
Ligands and binding sites
- MG · Magnesium ion · metal · 19 copies · chains C, E, D, F, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 892 | 0.77 | 0.81 | 60 | MG |
| 2 | 901 | 0.76 | 0.80 | 61 | MG |
| 3 | 52 | 0.70 | 0.98 | 17 | empty |
| 4 | 134 | 0.42 | 0.76 | 21 | empty |
| 5 | 89 | 0.37 | 0.76 | 17 | empty |
Interfaces
14 interfaces between chains.
- A–B · 1298 Ų buried · 20 hydrogen bonds · protein-protein
- C–B · 502 Ų buried · 18 hydrogen bonds · protein-nucleic
- D–A · 499 Ų buried · 19 hydrogen bonds · protein-nucleic
- C–E · 495 Ų buried · 39 hydrogen bonds · nucleic-nucleic
- D–F · 494 Ų buried · 40 hydrogen bonds · nucleic-nucleic
Compared structures
- 2NUG · Crystal structure of RNase III from Aquifex aeolicus complexed with ds-RNA at… · the same entry in another collection · chain B against B, TM-score 1.00
- O67082 · AlphaFold monomer V2.0 prediction for ribonuclease 3 (O67082) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 2NUG · PDBe 2NUG · UniProt O67082
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