Research workbench
Acylaminoacyl peptidase in complex with Z-gly-gly-phe-chloromethyl ketone
Analyse Acylaminoacyl peptidase in complex with Z-gly-gly-phe-chloromethyl ketone in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HXF
- Type
- protein
- Length
- 613 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative uncharacterized protein PH0594
- EC
- 3.4.19.1
- UniProt
- O58323
- Ligands
- Y3A, MG, CL
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 19% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Putative uncharacterized protein PH0594 (EC 3.4.19.1) | protein | 613 | 19% helix, 40% strand | O58323 |
Ligands and binding sites
- Y3A · N-[(benzyloxy)carbonyl]glycyl-N-[(2S,3R)-4-chloro-3-hydroxy-1-phenylbutan-2-yl]glycinamide · ligand · chains B
- MG · Magnesium ion · metal · 5 copies · chains B
- CL · Chloride ion · ion · chains B
- HEZ · Hexane-1,6-diol · additive · 10 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 644 | 0.76 | 0.82 | 79 | Y3A, MG, HEZ |
| 2 | 406 | 0.70 | 0.82 | 52 | HEZ |
| 3 | 77 | 0.37 | 0.77 | 15 | empty |
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4HXF · Acylaminoacyl peptidase in complex with Z-Gly-Gly-Phe-chloromethyl ketone · the same entry in another collection · chain B against B, TM-score 1.00
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 O58323
- Elsewhere: RCSB PDB 4HXF · PDBe 4HXF · UniProt O58323
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