MolNFT v1 · #162455 · protein + RNA
Structure of saccharomyces cerevisiae apo PAN2 pseudoubiquitin hydrolase-RNA exonuclease (uch-exo) module in complex with aauuaa RNA
6R9P · PAN2-PAN3 deadenylation complex catalytic subunit PAN2: “Structure of saccharomyces cerevisiae apo PAN2 pseudoubiquitin hydrolase-RNA exonuclease (uch-exo) module in…”. X-ray diffraction, 7 pockets (best druggability 0.73). MolNFT…
- PDB
- 6R9P
- Type
- protein + RNA
- Length
- 611 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PAN2-PAN3 deadenylation complex catalytic subunit PAN2; Aauuaa RNA
- EC
- 3.1.13.4
- UniProt
- P53010
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | PAN2-PAN3 deadenylation complex catalytic subunit PAN2 (EC 3.1.13.4) | protein | 607 | 28% helix, 22% strand | P53010 |
| B | Aauuaa RNA | rna | 4 | — | — |
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 69 | 0.73 | 0.97 | 16 | empty |
| 2 | 741 | 0.72 | 0.78 | 70 | empty |
| 3 | 229 | 0.65 | 0.84 | 32 | empty |
| 4 | 125 | 0.61 | 0.85 | 21 | empty |
| 5 | 167 | 0.47 | 0.76 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 495 Ų buried · 11 hydrogen bonds · protein-nucleic
Compared structures
- 6R9P · Structure of Saccharomyces cerevisiae apo Pan2 pseudoubiquitin hydrolase-RNA exonuclease… · the same entry in another collection · chain A against A, TM-score 1.00
- P53010 · AlphaFold monomer V2.0 prediction for PAN2-PAN3 deadenylation complex catalytic subunit… · 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 P53010
- Elsewhere: RCSB PDB 6R9P · PDBe 6R9P · UniProt P53010
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