Research workbench
RNase II D209N mutant
Analyse RNase II D209N mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IX1
- Type
- protein + RNA
- Length
- 656 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exoribonuclease 2; 5'-D(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP *AP*AP*A)-3'
- EC
- 3.1.13.1
- UniProt
- P30850
- Ligands
- MG
- Pockets
- 8 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Exoribonuclease 2 (EC 3.1.13.1) | protein | 643 | 30% helix, 31% strand | P30850 |
| B | 5'-D(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP *AP*AP*A)-3' | rna | 13 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1068 | 0.85 | 0.86 | 86 | empty |
| 2 | 204 | 0.75 | 0.91 | 27 | empty |
| 3 | 390 | 0.66 | 0.80 | 43 | empty |
| 4 | 124 | 0.45 | 0.78 | 25 | empty |
| 5 | 132 | 0.42 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2100 Ų buried · 47 hydrogen bonds · protein-nucleic
Compared structures
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 P30850
- Elsewhere: RCSB PDB 2IX1 · PDBe 2IX1 · UniProt P30850
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