Research workbench
Crystal structure of RNase III from Aquifex Aeolicus complexed with double-stranded RNA at 2.5-angstrom resolution
Analyse Crystal structure of RNase III from Aquifex Aeolicus complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YYK
- Type
- protein + RNA
- Length
- 490 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.5
- Source
- Aquifex aeolicus; SYNTHETIC CONSTRUCT
- 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
- 4 · best druggability 0.63
Structure
x-ray diffraction · resolution 2.5 · 2 distinct chains · 57% helix, 11% 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, B | Ribonuclease III (EC 3.1.26.3) | protein | 221 | 57% helix, 11% strand | O67082 |
Ligands and binding sites
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 790 | 0.63 | 0.73 | 64 | empty |
| 2 | 300 | 0.51 | 0.73 | 36 | empty |
| 3 | 293 | 0.50 | 0.73 | 23 | empty |
| 4 | 53 | 0.30 | 0.76 | 14 | empty |
Interfaces
13 interfaces between chains.
- A–B · 1390 Ų buried · 28 hydrogen bonds · protein-protein
- E–F · 613 Ų buried · 61 hydrogen bonds · nucleic-nucleic
- C–D · 597 Ų buried · 64 hydrogen bonds · nucleic-nucleic
- C–A · 314 Ų buried · 13 hydrogen bonds · protein-nucleic
- F–A · 280 Ų buried · 7 hydrogen bonds · protein-nucleic
Compared structures
- 1YYK · Crystal structure of RNase III from aquifex aeolicus complexed with double-stranded RNA… · 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 0.72
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 1YYK · PDBe 1YYK · UniProt O67082
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