MolNFT v1 · #125718 · protein
Structure of glycosylated human aminopeptidase N
5LHD: “Structure of glycosylated human aminopeptidase N”. X-ray diffraction, 3 ligands (NAG, BMA, ZN), 20 pockets (best druggability 0.74). MolNFT v1 #125718 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5LHD
- Type
- protein
- Length
- 3,616 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminopeptidase N
- EC
- 3.4.11.2
- UniProt
- P15144
- Ligands
- NAG, BMA, ZN
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aminopeptidase N (EC 3.4.11.2) | protein | 903 | 46% helix, 21% strand | P15144 |
| B, D | Aminopeptidase N (EC 3.4.11.2) | protein | 904 | 46% helix, 19% strand | P15144 |
| C | Aminopeptidase N (EC 3.4.11.2) | protein | 905 | 46% helix, 20% strand | P15144 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 64 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar · 37 copies · chains C, A, D, B
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 46 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 843 | 0.74 | 0.78 | 67 | empty |
| 2 | 809 | 0.73 | 0.78 | 71 | EDO |
| 3 | 901 | 0.73 | 0.77 | 84 | EDO |
| 4 | 595 | 0.73 | 0.80 | 65 | EDO |
| 5 | 939 | 0.73 | 0.77 | 87 | EDO |
Interfaces
4 interfaces between chains.
- B–C · 388 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 348 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 268 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 63 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 35 glycan, 8 disulfide (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 P15144
- Elsewhere: RCSB PDB 5LHD · PDBe 5LHD · UniProt P15144
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