Research workbench
Crystal structure of human aminopeptidase a complexed with aspartate and calcium
Analyse Crystal structure of human aminopeptidase a complexed with aspartate and calcium in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KXA
- 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
- ASP, NAG, CA, ZN
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamyl aminopeptidase (EC 3.4.11.7) | protein | 875 | 46% helix, 21% strand | Q07075 |
Ligands and binding sites
- ASP · Aspartic acid · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains A
- CA · Calcium ion · metal · chains A
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 707 | 0.81 | 0.85 | 106 | CA, ASP |
| 2 | 72 | 0.66 | 0.93 | 18 | empty |
| 3 | 171 | 0.59 | 0.82 | 30 | empty |
| 4 | 130 | 0.59 | 0.85 | 36 | empty |
| 5 | 72 | 0.32 | 0.75 | 13 | empty |
Modifications
Observed in the structure: 8 glycan, 1 disulfide (N-glycosylation, disulfide).
Compared structures
- 4KXA · Crystal structure of human aminopeptidase A complexed with aspartate and calcium · 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 4KXA · PDBe 4KXA · UniProt Q07075
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