MolNFT v1 · #98040 · protein
Crystal structure of human aminopeptidase a complexed with amastatin
4KX8 · Glutamyl aminopeptidase: “Crystal structure of human aminopeptidase a complexed with amastatin”. X-ray diffraction, 3 ligands (L2O, NAG, ZN), 6 pockets (best druggability 0.77). MolNFT v1 #98040 on GenesisL1: 3D structure, binding…
- PDB
- 4KX8
- Type
- protein
- Length
- 878 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamyl aminopeptidase; Amastatin
- EC
- 3.4.11.7
- UniProt
- Q07075
- Ligands
- L2O, NAG, ZN
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 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 |
| C | Amastatin | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- L2O · (2S,3R)-3-amino-2-hydroxy-5-methylhexanoic acid · ligand · chains A, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains A
- ZN · Zinc ion · metal · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 627 | 0.77 | 0.83 | 84 | empty |
| 2 | 287 | 0.75 | 0.88 | 58 | empty |
| 3 | 77 | 0.66 | 0.93 | 19 | empty |
| 4 | 180 | 0.61 | 0.83 | 32 | empty |
| 5 | 70 | 0.32 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–C · 340 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 glycan, 1 covalent, 1 disulfide (N-glycosylation, covalent ligand, disulfide).
Compared structures
- 4KX8 · Crystal structure of human aminopeptidase A complexed with amastatin · 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 4KX8 · PDBe 4KX8 · UniProt Q07075
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.