Research workbench
Crystal structure of X-prolyl aminopeptidase from caenorhabditis elegans: a cytosolic enzyme with a di-nuclear active site
Analyse Crystal structure of X-prolyl aminopeptidase from caenorhabditis elegans: a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4S2R
- Type
- protein
- Length
- 1,227 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein app-1
- EC
- 3.4.11.9
- UniProt
- O44750
- Ligands
- ZN
- Pockets
- 13 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P | Protein app-1 (EC 3.4.11.9) | protein | 615 | 41% helix, 19% strand | O44750 |
| Q | Protein app-1 (EC 3.4.11.9) | protein | 612 | 41% helix, 20% strand | O44750 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains P, Q
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 961 | 0.79 | 0.81 | 97 | ZN |
| 2 | 1001 | 0.77 | 0.79 | 110 | empty |
| 3 | 329 | 0.68 | 0.82 | 34 | empty |
| 4 | 338 | 0.63 | 0.79 | 30 | empty |
| 5 | 252 | 0.57 | 0.78 | 37 | empty |
Interfaces
1 interface between chains.
- P–Q · 2099 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 4S2R · Crystal structure of X-prolyl aminopeptidase from Caenorhabditis elegans: a cytosolic… · the same entry in another collection · chain P against P, TM-score 1.00
- O44750 · AlphaFold monomer V2.0 prediction for xaa-pro aminopeptidase app-1 (O44750) · a predicted model of the same protein · chain Q 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 O44750
- Elsewhere: RCSB PDB 4S2R · PDBe 4S2R · UniProt O44750
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.