Research workbench
RNA degradation enzyme
Analyse RNA degradation enzyme in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OPK
- Type
- protein
- Length
- 649 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-3' exoribonuclease
- EC
- 3.1.13.-
- UniProt
- G0S058
- Ligands
- MG
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'-3' exoribonuclease (EC 3.1.13.-) | protein | 649 | 44% helix, 10% strand | G0S058 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1054 | 0.82 | 0.83 | 91 | MG |
| 2 | 276 | 0.56 | 0.77 | 35 | empty |
| 3 | 172 | 0.45 | 0.75 | 32 | empty |
| 4 | 51 | 0.43 | 0.84 | 16 | empty |
| 5 | 95 | 0.43 | 0.78 | 19 | empty |
Compared structures
- 7OPK · Crystal structure of C. thermophilum Xrn2 · the same entry in another collection · chain A against A, TM-score 1.00
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 G0S058
- Elsewhere: RCSB PDB 7OPK · PDBe 7OPK · UniProt G0S058
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