MolNFT v1 · #162454 · protein + RNA
Structure of saccharomyces cerevisiae apo PAN2 pseudoubiquitin hydrolase-RNA exonuclease (uch-exo) module in complex with aagga RNA
6R9O · 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 0.75). MolNFT…
- PDB
- 6R9O
- Type
- protein + RNA
- Length
- 598 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PAN2-PAN3 deadenylation complex catalytic subunit PAN2; Aagga RNA
- EC
- 3.1.13.4
- UniProt
- P53010
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 30% 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 | 594 | 30% helix, 22% strand | P53010 |
| B | Aagga RNA | rna | 4 | — | — |
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 | 1043 | 0.75 | 0.77 | 93 | empty |
| 2 | 108 | 0.62 | 0.87 | 30 | empty |
| 3 | 181 | 0.51 | 0.78 | 24 | empty |
| 4 | 86 | 0.49 | 0.82 | 19 | empty |
| 5 | 122 | 0.44 | 0.77 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 528 Ų buried · 11 hydrogen bonds · protein-nucleic
Compared structures
- 6R9O · 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 6R9O · PDBe 6R9O · UniProt P53010
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