MolNFT v1 · #48267 · protein
Crystal structure of the P. abyssi exosome RNase pH ring complexed with udp and gmp
2PNZ · Probable exosome complex exonuclease 1: “Crystal structure of the P. abyssi exosome RNase pH ring complexed with udp and gmp”. X-ray diffraction, 2 ligands (UDP, 5GP), 3 pockets (best druggability 0.55). MolNFT v1 #48267 on…
- PDB
- 2PNZ
- Type
- protein
- Length
- 503 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable exosome complex exonuclease 1; Probable exosome complex exonuclease 2
- EC
- 3.1.13.-
- UniProt
- Q9V119, Q9V118
- Ligands
- UDP, 5GP
- Pockets
- 3 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable exosome complex exonuclease 1 (EC 3.1.13.-) | protein | 236 | 32% helix, 31% strand | Q9V119 |
| B | Probable exosome complex exonuclease 2 (EC 3.1.13.-) | protein | 267 | 30% helix, 34% strand | Q9V118 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · chains A
- 5GP · Guanosine-5'-monophosphate · ligand · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 131 | 0.55 | 0.82 | 19 | empty |
| 2 | 122 | 0.50 | 0.80 | 16 | empty |
| 3 | 126 | 0.44 | 0.77 | 25 | UDP |
Interfaces
1 interface between chains.
- A–B · 1195 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 2PNZ · Crystal structure of the P. abyssi exosome RNase PH ring complexed with UDP and GMP · the same entry in another collection · chain A against A, TM-score 1.00
- Q9V119 · AlphaFold monomer V2.0 prediction for exosome complex component RRP41 (Q9V119) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q9V118 · AlphaFold monomer V2.0 prediction for exosome complex component RRP42 (Q9V118) · a predicted model of the same protein · chain B 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 Q9V119
- Every structure of UniProt Q9V118
- Elsewhere: RCSB PDB 2PNZ · PDBe 2PNZ · UniProt Q9V119 · UniProt Q9V118
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