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Crystal structure of RNase III mutant E110Q from aquifex aeolicus complexed with double stranded RNA at 2.1-ångström resolution
Analyse Crystal structure of RNase III mutant E110Q from aquifex aeolicus complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YZ9
- Type
- protein + RNA
- Length
- 482 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(*CP*GP*AP*AP*CP*UP*UP*CP*GP*CP*G)-3'; Ribonuclease III
- EC
- 3.1.26.3
- UniProt
- O67082
- Ligands
- SO4
- Pockets
- 2 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 61% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D, E, F | 5'-R(*CP*GP*AP*AP*CP*UP*UP*CP*GP*CP*G)-3' | rna | 11 | — | — |
| A | Ribonuclease III (EC 3.1.26.3) | protein | 220 | 60% helix, 11% strand | O67082 |
| B | Ribonuclease III (EC 3.1.26.3) | protein | 218 | 61% helix, 11% strand | O67082 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 7 copies · chains D, E, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 641 | 0.59 | 0.72 | 41 | SO4 |
| 2 | 67 | 0.46 | 0.84 | 17 | empty |
Interfaces
10 interfaces between chains.
- A–B · 1206 Ų buried · 23 hydrogen bonds · protein-protein
- C–A · 490 Ų buried · 15 hydrogen bonds · protein-nucleic
- E–F · 458 Ų buried · 43 hydrogen bonds · nucleic-nucleic
- C–D · 457 Ų buried · 37 hydrogen bonds · nucleic-nucleic
- D–A · 354 Ų buried · 7 hydrogen bonds · protein-nucleic
Compared structures
- 1YZ9 · Crystal structure of RNase III mutant E110Q from Aquifex aeolicus complexed with double… · 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 0.71
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 1YZ9 · PDBe 1YZ9 · UniProt O67082
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