Research workbench
Crystal structure of aquifex aeolicus RNase III (D44N) complexed with product of double-stranded RNA processing
Analyse Crystal structure of aquifex aeolicus RNase III (D44N) complexed with product… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2EZ6
- Type
- protein + RNA
- Length
- 492 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 28-mer; Ribonuclease III
- EC
- 3.1.26.3
- UniProt
- O67082
- Ligands
- MG
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 59% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | 28-mer | rna | 28 | — | — |
| A, B | Ribonuclease III (EC 3.1.26.3) | protein | 218 | 59% helix, 11% strand | O67082 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains C, A, D, 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 672 | 0.83 | 0.88 | 75 | empty |
| 2 | 127 | 0.52 | 0.82 | 18 | empty |
| 3 | 77 | 0.48 | 0.84 | 18 | empty |
| 4 | 92 | 0.45 | 0.81 | 12 | empty |
| 5 | 84 | 0.32 | 0.74 | 17 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1172 Ų buried · 20 hydrogen bonds · protein-protein
- D–A · 684 Ų buried · 24 hydrogen bonds · protein-nucleic
- C–A · 680 Ų buried · 13 hydrogen bonds · protein-nucleic
- C–B · 675 Ų buried · 24 hydrogen bonds · protein-nucleic
- D–B · 669 Ų buried · 12 hydrogen bonds · protein-nucleic
Compared structures
- 2EZ6 · Crystal structure of Aquifex aeolicus RNase III (D44N) complexed with product of… · 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 0.86
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 2EZ6 · PDBe 2EZ6 · UniProt O67082
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