Research workbench
Insulin-regulated aminopeptidase complexed with a macrocyclic peptidic inhibitor
Analyse Insulin-regulated aminopeptidase complexed with a macrocyclic peptidic inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YDX
- 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
- ONN, NAG, BMA, ZN, PO4
- Pockets
- 15 · best druggability 0.83
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 | 856 | 46% helix, 21% strand | Q9UIQ6 |
| B | Leucyl-cystinyl aminopeptidase (EC 3.4.11.3) | protein | 853 | 47% helix, 23% strand | Q9UIQ6 |
Ligands and binding sites
- ONN · 2-[2-[[[(4~{R},8~{S},11~{S})-11-azanyl-8-[(4-hydroxyphenyl)methyl]-6,10-bis(oxidanylidene)-1,2-dithia-5,9-diazacyclotridec-4-yl]carbonylamino]methyl]phenyl]ethanoic acid · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 24 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies
- ZN · Zinc ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
- SIN · Succinic acid · additive · chains A
- PGE · Triethylene glycol · additive
- PG4 · Tetraethylene glycol · additive
- PEG · Di(hydroxyethyl)ether · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 544 | 0.83 | 0.88 | 55 | empty |
| 2 | 850 | 0.82 | 0.84 | 92 | ONN, ZN |
| 3 | 504 | 0.81 | 0.88 | 48 | empty |
| 4 | 508 | 0.79 | 0.86 | 44 | ONN |
| 5 | 359 | 0.71 | 0.83 | 43 | empty |
Interfaces
1 interface between chains.
- A–B · 135 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 glycan, 1 disulfide (N-glycosylation, disulfide, glycosylation).
Compared structures
- 6YDX · Insulin-regulated aminopeptidase complexed with a macrocyclic peptidic inhibitor · 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 0.99
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 6YDX · PDBe 6YDX · UniProt Q9UIQ6
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