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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
- 4S2T
- Type
- protein
- Length
- 1,233 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein app-1; Apstatin
- UniProt
- O44750
- Ligands
- 01B, ZN, SO4
- Pockets
- 16 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P | Protein app-1 | protein | 615 | 41% helix, 21% strand | O44750 |
| Q | Protein app-1 | protein | 612 | 42% helix, 20% strand | O44750 |
| A, B | Apstatin | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- 01B · (2S,3R)-3-amino-2-hydroxy-4-phenylbutanoic acid · ligand · 2 copies · chains P, A, Q, B
- ZN · Zinc ion · metal · 4 copies · chains P, A, Q, B
- SO4 · Sulfate ion · ion · 7 copies · chains P, Q
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1170 | 0.78 | 0.80 | 98 | empty |
| 2 | 590 | 0.70 | 0.78 | 61 | empty |
| 3 | 422 | 0.69 | 0.81 | 41 | empty |
| 4 | 475 | 0.66 | 0.78 | 46 | SO4 |
| 5 | 346 | 0.62 | 0.78 | 38 | empty |
Interfaces
3 interfaces between chains.
- P–Q · 2037 Ų buried · 14 hydrogen bonds · protein-protein
- P–A · 305 Ų buried · 4 hydrogen bonds · protein-protein
- Q–B · 281 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4S2T · 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 4S2T · PDBe 4S2T · UniProt O44750
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