Research workbench
Structure of the saccharomyces cerevisiae PAN2 pseudoubiquitin- hydrolase-RNase module
Analyse Structure of the saccharomyces cerevisiae PAN2 pseudoubiquitin- hydrolase-RNase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Q8H
- Type
- protein
- Length
- 627 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pab-dependent POLY(A)-specific ribonuclease subunit PAN2
- EC
- 3.1.13.4
- UniProt
- P53010
- Ligands
- MG
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pab-dependent POLY(A)-specific ribonuclease subunit PAN2 (EC 3.1.13.4) | protein | 627 | 30% helix, 22% strand | P53010 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1033 | 0.77 | 0.79 | 96 | MG |
| 2 | 405 | 0.69 | 0.82 | 39 | empty |
| 3 | 69 | 0.58 | 0.88 | 19 | empty |
| 4 | 317 | 0.55 | 0.75 | 39 | empty |
| 5 | 63 | 0.48 | 0.84 | 16 | empty |
Compared structures
- 4Q8H · Structure of the Saccharomyces cerevisiae PAN2 pseudoubiquitin-hydrolase-RNase module · 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 0.97
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 4Q8H · PDBe 4Q8H · UniProt P53010
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