MolNFT v1 · #103906 · protein
Crystal structure of the arabidopsis thaliana TOP2 oligopeptidase
4PUT · Cytosolic oligopeptidase a: “Crystal structure of the arabidopsis thaliana TOP2 oligopeptidase”. X-ray diffraction, 2 ligands (ZN, CL), 7 pockets (best druggability 0.76). MolNFT v1 #103906 on GenesisL1: 3D structure, binding sites…
- PDB
- 4PUT
- Type
- protein
- Length
- 692 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytosolic oligopeptidase a
- EC
- 3.4.24.70
- UniProt
- Q949P2
- Ligands
- ZN, CL
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 60% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytosolic oligopeptidase a (EC 3.4.24.70) | protein | 692 | 60% helix, 8% strand | Q949P2 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 938 | 0.76 | 0.79 | 81 | empty |
| 2 | 669 | 0.66 | 0.75 | 70 | empty |
| 3 | 211 | 0.53 | 0.77 | 26 | empty |
| 4 | 71 | 0.46 | 0.82 | 15 | empty |
| 5 | 59 | 0.31 | 0.75 | 14 | empty |
Compared structures
- 4PUT · Crystal structure of the Arabidopsis thaliana TOP2 oligopeptidase · the same entry in another collection · chain A against A, TM-score 1.00
- Q949P2 · AlphaFold monomer V2.0 prediction for probable cytosolic oligopeptidase a (Q949P2) · a predicted model of the same protein · chain A against A, TM-score 0.78
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 Q949P2
- Elsewhere: RCSB PDB 4PUT · PDBe 4PUT · UniProt Q949P2
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