Research workbench
Crystal structure of legionella pneumophila aminopeptidase a in complex with aspartic acid
Analyse Crystal structure of legionella pneumophila aminopeptidase a in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZIE
- Type
- protein
- Length
- 1,700 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminopeptidase N
- EC
- 3.4.11.2
- UniProt
- Q5ZVE3
- Ligands
- ASP
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Aminopeptidase N (EC 3.4.11.2) | protein | 850 | 43% helix, 23% strand | Q5ZVE3 |
Ligands and binding sites
- ASP · Aspartic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1013 | 0.83 | 0.84 | 110 | ASP |
| 2 | 459 | 0.77 | 0.85 | 51 | empty |
| 3 | 201 | 0.70 | 0.88 | 44 | ASP |
| 4 | 119 | 0.69 | 0.91 | 22 | empty |
| 5 | 148 | 0.69 | 0.89 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 770 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5ZIE · Crystal structure of Legionella pneumophila aminopeptidase A in complex with aspartic acid · the same entry in another collection · 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 Q5ZVE3
- Elsewhere: RCSB PDB 5ZIE · PDBe 5ZIE · UniProt Q5ZVE3
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