Research workbench
Structure of the porcine aminopeptidase N ectodomain
Analyse Structure of the porcine aminopeptidase N ectodomain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LDS
- Type
- protein
- Length
- 3,595 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminopeptidase N
- EC
- 3.4.11.2
- UniProt
- P15145
- Ligands
- NAG, BMA, ZN
- Pockets
- 20 · best druggability 0.83
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 | 900 | 46% helix, 20% strand | P15145 |
| B, D | Aminopeptidase N (EC 3.4.11.2) | protein | 898 | 46% helix, 20% strand | P15145 |
| C | Aminopeptidase N (EC 3.4.11.2) | protein | 899 | 46% helix, 20% strand | P15145 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 46 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar · 6 copies · chains D, A
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 4 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1012 | 0.83 | 0.84 | 109 | ACT |
| 2 | 1100 | 0.82 | 0.84 | 116 | ACT |
| 3 | 1022 | 0.82 | 0.84 | 108 | ACT |
| 4 | 1046 | 0.82 | 0.83 | 111 | ACT |
| 5 | 858 | 0.79 | 0.81 | 67 | empty |
Interfaces
1 interface between chains.
- A–B · 1027 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 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 P15145
- Elsewhere: RCSB PDB 5LDS · PDBe 5LDS · UniProt P15145
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