MolNFT v1 · #111992 · protein
Crystal structure of insulin regulated aminopeptidase in complex with ligand
4Z7I · Leucyl-cystinyl aminopeptidase: “Crystal structure of insulin regulated aminopeptidase in complex with ligand”. X-ray diffraction, 5 ligands (2X0, 4L8, NAG), 13 pockets (best druggability 0.85). MolNFT v1 #111992 on GenesisL1: 3D…
- PDB
- 4Z7I
- Type
- protein
- Length
- 1,722 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Leucyl-cystinyl aminopeptidase; DG025 transition-state analogue enzyme inhibitor
- EC
- 3.4.11.3
- UniProt
- Q9UIQ6
- Ligands
- 2X0, 4L8, NAG, MAN, ZN
- Pockets
- 13 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Leucyl-cystinyl aminopeptidase (EC 3.4.11.3) | protein | 859 | 44% helix, 19% strand | Q9UIQ6 |
| B | Leucyl-cystinyl aminopeptidase (EC 3.4.11.3) | protein | 852 | 42% helix, 17% strand | Q9UIQ6 |
| C | DG025 transition-state analogue enzyme inhibitor | protein | 8 | 0% helix, 0% strand | — |
| D | DG025 transition-state analogue enzyme inhibitor | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- 2X0 · [(1R)-1-amino-3-phenylpropyl]phosphonic acid · ligand · 2 copies · chains A, C, B, D
- 4L8 · (2R)-2-(aminomethyl)-4-methylpentanoic acid · ligand · 2 copies · chains A, C, B, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 27 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar
- 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
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 949 | 0.85 | 0.86 | 92 | 2X0, 4L8 |
| 2 | 463 | 0.83 | 0.90 | 68 | 2X0, 4L8 |
| 3 | 317 | 0.82 | 0.92 | 36 | empty |
| 4 | 537 | 0.75 | 0.83 | 75 | empty |
| 5 | 305 | 0.64 | 0.80 | 53 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1214 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 688 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 210 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 glycan, 2 covalent, 2 disulfide (N-glycosylation, covalent ligand, disulfide).
Compared structures
- 4Z7I · Crystal structure of insulin regulated aminopeptidase in complex with ligand · 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 4Z7I · PDBe 4Z7I · UniProt Q9UIQ6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.