MolNFT v1 · #162449 · protein + RNA
Structure of saccharomyces cerevisiae apo PAN2 pseudoubiquitin hydrolase-RNA exonuclease (uch-exo) module in complex with A7 RNA
6R9J · PAN2-PAN3 deadenylation complex catalytic subunit PAN2: “Structure of saccharomyces cerevisiae apo PAN2 pseudoubiquitin hydrolase-RNA exonuclease (uch-exo) module in…”. X-ray diffraction, 6 pockets (best druggability 0.74). MolNFT…
- PDB
- 6R9J
- Type
- protein + RNA
- Length
- 600 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PAN2-PAN3 deadenylation complex catalytic subunit PAN2; A7 RNA
- EC
- 3.1.13.4
- UniProt
- P53010
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 31% 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 | 595 | 31% helix, 22% strand | P53010 |
| B | A7 RNA | rna | 5 | — | — |
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1195 | 0.74 | 0.77 | 101 | empty |
| 2 | 101 | 0.57 | 0.85 | 23 | empty |
| 3 | 85 | 0.54 | 0.85 | 20 | empty |
| 4 | 92 | 0.41 | 0.78 | 20 | empty |
| 5 | 97 | 0.41 | 0.77 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 585 Ų buried · 11 hydrogen bonds · protein-nucleic
Compared structures
- 6R9J · 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 6R9J · PDBe 6R9J · UniProt P53010
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