MolNFT v1 · #38859 · protein
Structure of the yeast nuclear exosome component, RRP6P, reveals an interplay between the active site and the hrdc domain; protein in complex with mn, zn, and ump
2HBM · Exosome complex exonuclease RRP6: “Structure of the yeast nuclear exosome component, RRP6P, reveals an interplay between the active site and the…”. X-ray diffraction, 3 ligands (U, ZN, MN), 4 pockets (best druggability 0.68). MolNFT…
- PDB
- 2HBM
- Type
- protein
- Length
- 390 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exosome complex exonuclease RRP6
- EC
- 3.1.13.-
- UniProt
- Q12149
- Ligands
- U, ZN, MN
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Exosome complex exonuclease RRP6 (EC 3.1.13.-) | protein | 390 | 42% helix, 9% strand | Q12149 |
Ligands and binding sites
- U · Uridine-5'-monophosphate · ligand · chains A
- ZN · Zinc ion · metal · chains A
- MN · Manganese (II) ion · metal · chains A
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 | 490 | 0.68 | 0.79 | 59 | ZN, MN, U |
| 2 | 237 | 0.61 | 0.80 | 30 | empty |
| 3 | 95 | 0.35 | 0.74 | 17 | empty |
| 4 | 74 | 0.32 | 0.74 | 17 | empty |
Compared structures
- 2HBM · Structure of the yeast nuclear exosome component, Rrp6p, reveals an interplay between the… · the same entry in another collection · chain A against A, TM-score 1.00
- Q12149 · AlphaFold monomer V2.0 prediction for exosome complex exonuclease RRP6 (Q12149) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q12149
- Elsewhere: RCSB PDB 2HBM · PDBe 2HBM · UniProt Q12149
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