Research workbench
Crystal structure of RNase III mutant E110K from aquifex aeolicus complexed with ds-RNA at 2.15 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
- 1RC7
- Type
- protein + RNA
- Length
- 260 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(*GP*GP*CP*GP*CP*GP*CP*GP*CP*C)-3'; Ribonuclease III
- EC
- 3.1.26.3
- UniProt
- O67082
- Pockets
- 2 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 60% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, C, D, E | 5'-R(*GP*GP*CP*GP*CP*GP*CP*GP*CP*C)-3' | rna | 10 | — | — |
| A | Ribonuclease III (EC 3.1.26.3) | protein | 220 | 60% helix, 11% strand | O67082 |
Ligands and binding sites
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
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 | 286 | 0.56 | 0.77 | 29 | empty |
| 2 | 240 | 0.42 | 0.71 | 26 | empty |
Interfaces
9 interfaces between chains.
- B–C · 506 Ų buried · 62 hydrogen bonds · nucleic-nucleic
- D–E · 499 Ų buried · 55 hydrogen bonds · nucleic-nucleic
- D–A · 416 Ų buried · 14 hydrogen bonds · protein-nucleic
- E–A · 254 Ų buried · 6 hydrogen bonds · protein-nucleic
- C–A · 235 Ų buried · 4 hydrogen bonds · protein-nucleic
Compared structures
- 1RC7 · Crystal structure of RNase III Mutant E110K from Aquifex Aeolicus complexed with ds-RNA… · 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 A 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 1RC7 · PDBe 1RC7 · UniProt O67082
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