Research workbench
Structure of saccharomyces cerevisiae apo PAN2 pseudoubiquitin hydrolase-RNA exonuclease (uch-exo) module in complex with aaggaa RNA
Analyse Structure of saccharomyces cerevisiae apo PAN2 pseudoubiquitin hydrolase-RNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6R9M
- Type
- protein + RNA
- Length
- 604 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PAN2-PAN3 deadenylation complex catalytic subunit PAN2; Aaggaa RNA
- EC
- 3.1.13.4
- UniProt
- P53010
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | PAN2-PAN3 deadenylation complex catalytic subunit PAN2 (EC 3.1.13.4) | protein | 600 | 31% helix, 21% strand | P53010 |
| B | Aaggaa RNA | rna | 4 | — | — |
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 739 | 0.75 | 0.80 | 77 | empty |
| 2 | 190 | 0.57 | 0.81 | 28 | empty |
| 3 | 158 | 0.46 | 0.76 | 25 | empty |
| 4 | 62 | 0.45 | 0.83 | 19 | empty |
| 5 | 103 | 0.40 | 0.76 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 520 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 6R9M · 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 6R9M · PDBe 6R9M · UniProt P53010
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