Research workbench
Crystal structure of human insulin regulated aminopeptidase with lysine in active site
Analyse Crystal structure of human insulin regulated aminopeptidase with lysine in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PJ6
- Type
- protein
- Length
- 1,709 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Leucyl-cystinyl aminopeptidase
- EC
- 3.4.11.3
- UniProt
- Q9UIQ6
- Ligands
- LYS, NAG, ZN
- Pockets
- 18 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Leucyl-cystinyl aminopeptidase (EC 3.4.11.3) | protein | 860 | 47% helix, 22% strand | Q9UIQ6 |
| B | Leucyl-cystinyl aminopeptidase (EC 3.4.11.3) | protein | 849 | 45% helix, 21% strand | Q9UIQ6 |
Ligands and binding sites
- LYS · Lysine · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 17 copies · chains B, A
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1000 | 0.81 | 0.82 | 106 | empty |
| 2 | 390 | 0.78 | 0.87 | 48 | empty |
| 3 | 309 | 0.70 | 0.84 | 38 | empty |
| 4 | 233 | 0.63 | 0.82 | 42 | empty |
| 5 | 174 | 0.60 | 0.82 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 1152 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 glycan, 2 disulfide (N-glycosylation, disulfide).
Compared structures
- 4PJ6 · Crystal Structure of Human Insulin Regulated Aminopeptidase with Lysine in Active Site · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UIQ6 · AlphaFold monomer V2.0 prediction for leucyl-cystinyl aminopeptidase (Q9UIQ6) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 Q9UIQ6
- Elsewhere: RCSB PDB 4PJ6 · PDBe 4PJ6 · UniProt Q9UIQ6
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