Research workbench
Crystal structure of human aminopeptidase a complexed with bestatin
Analyse Crystal structure of human aminopeptidase a complexed with bestatin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KXB
- Type
- protein
- Length
- 875 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamyl aminopeptidase
- EC
- 3.4.11.7
- UniProt
- Q07075
- Ligands
- BES, NAG, ZN
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamyl aminopeptidase (EC 3.4.11.7) | protein | 875 | 47% helix, 21% strand | Q07075 |
Ligands and binding sites
- BES · 2-(3-amino-2-hydroxy-4-phenyl-butyrylamino)-4-methyl-pentanoic acid · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 15 copies · chains A
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 819 | 0.82 | 0.85 | 107 | BES |
| 2 | 70 | 0.65 | 0.93 | 17 | empty |
| 3 | 175 | 0.62 | 0.84 | 29 | empty |
| 4 | 138 | 0.60 | 0.85 | 35 | empty |
| 5 | 92 | 0.39 | 0.77 | 25 | empty |
Modifications
Observed in the structure: 7 glycan (N-glycosylation).
Compared structures
- 4KXB · Crystal structure of human aminopeptidase A complexed with bestatin · the same entry in another collection · chain A against A, TM-score 1.00
- Q07075 · AlphaFold monomer V2.0 prediction for glutamyl aminopeptidase (Q07075) · a predicted model of the same protein · chain A against A, 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 Q07075
- Elsewhere: RCSB PDB 4KXB · PDBe 4KXB · UniProt Q07075
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