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Crystal structure of RNase III mutant E110K from aquifex aeolicus complexed with double-stranded RNA at 2.9-ångström resolution
Analyse Crystal structure of RNase III mutant E110K 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
- 1YYO
- Type
- protein + RNA
- Length
- 487 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(*CP*GP*CP*GP*AP*AP*UP*UP*CP*GP*CP*G)-3'; Ribonuclease III
- EC
- 3.1.26.3
- UniProt
- O67082
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 58% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D, E, F | 5'-R(*CP*GP*CP*GP*AP*AP*UP*UP*CP*GP*CP*G)-3' | rna | 12 | — | — |
| A | Ribonuclease III (EC 3.1.26.3) | protein | 220 | 55% helix, 11% strand | O67082 |
| B | Ribonuclease III (EC 3.1.26.3) | protein | 219 | 60% helix, 10% strand | O67082 |
Ligands and binding sites
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 826 | 0.63 | 0.72 | 63 | TRS |
| 2 | 321 | 0.53 | 0.74 | 32 | empty |
| 3 | 330 | 0.52 | 0.74 | 26 | empty |
Interfaces
13 interfaces between chains.
- A–B · 1414 Ų buried · 30 hydrogen bonds · protein-protein
- E–F · 583 Ų buried · 60 hydrogen bonds · nucleic-nucleic
- C–D · 576 Ų buried · 54 hydrogen bonds · nucleic-nucleic
- C–A · 300 Ų buried · 12 hydrogen bonds · protein-nucleic
- F–A · 292 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 1YYO · Crystal structure of RNase III mutant E110K from Aquifex aeolicus complexed with… · the same entry in another collection · chain A against A, 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 0.73
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 1YYO · PDBe 1YYO · UniProt O67082
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