MolNFT v1 · #152264 · protein
The crystal structure of legionella pneumophila lapa aminopeptidase
6ICA: “The crystal structure of legionella pneumophila lapa aminopeptidase”. X-ray diffraction, 2 ligands (ZN, SO4), 11 pockets (best druggability 0.79). MolNFT v1 #152264 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6ICA
- Type
- protein
- Length
- 1,115 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminopeptidase
- UniProt
- Q5ZRR6
- Ligands
- ZN, SO4
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aminopeptidase | protein | 366 | 39% helix, 19% strand | Q5ZRR6 |
| B | Aminopeptidase | protein | 371 | 39% helix, 19% strand | Q5ZRR6 |
| C | Aminopeptidase | protein | 378 | 38% helix, 19% strand | Q5ZRR6 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 9 copies · chains A, B, C
- GOL · Glycerol · additive · 5 copies · chains A, B, C
- ACT · Acetate ion · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 146 | 0.79 | 0.96 | 32 | empty |
| 2 | 176 | 0.78 | 0.94 | 33 | ZN |
| 3 | 185 | 0.77 | 0.93 | 34 | ZN |
| 4 | 994 | 0.72 | 0.76 | 102 | SO4 |
| 5 | 234 | 0.66 | 0.83 | 22 | empty |
Interfaces
2 interfaces between chains.
- B–C · 1602 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 334 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6ICA · The crystal structure of Legionella pneumophila LapA aminopeptidase · 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 Q5ZRR6
- Elsewhere: RCSB PDB 6ICA · PDBe 6ICA · UniProt Q5ZRR6
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