MolNFT v1 · #125678 · protein
Structure of the deglycosylated porcine aminopeptidase N ectodomain
5LG6: “Structure of the deglycosylated porcine aminopeptidase N ectodomain”. X-ray diffraction, 2 ligands (NAG, ZN), 13 pockets (best druggability 0.82). MolNFT v1 #125678 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5LG6
- Type
- protein
- Length
- 1,776 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminopeptidase N
- EC
- 3.4.11.2
- UniProt
- P15145
- Ligands
- NAG, ZN
- Pockets
- 13 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aminopeptidase N (EC 3.4.11.2) | protein | 889 | 47% helix, 20% strand | P15145 |
| B | Aminopeptidase N (EC 3.4.11.2) | protein | 887 | 47% helix, 20% strand | P15145 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 18 copies · chains A, B
- 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1174 | 0.82 | 0.83 | 112 | ZN |
| 2 | 1145 | 0.81 | 0.82 | 105 | ZN |
| 3 | 345 | 0.69 | 0.83 | 33 | empty |
| 4 | 338 | 0.68 | 0.82 | 33 | empty |
| 5 | 420 | 0.66 | 0.79 | 50 | empty |
Interfaces
1 interface between chains.
- A–B · 410 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 48 modified, 18 glycan, 4 disulfide (engineered, N-glycosylation, disulfide).
Compared structures
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 P15145
- Elsewhere: RCSB PDB 5LG6 · PDBe 5LG6 · UniProt P15145
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