Research workbench
Crystal structure of porcine aminopeptidase-N complexed with substance P
Analyse Crystal structure of porcine aminopeptidase-N complexed with substance P in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HOM
- Type
- protein
- Length
- 913 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminopeptidase N; Substance P
- EC
- 3.4.11.2
- UniProt
- P15145
- Ligands
- NAG, ZN
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aminopeptidase N (EC 3.4.11.2) | protein | 902 | 44% helix, 20% strand | P15145 |
| B | Substance P | protein | 11 | 0% helix, 0% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 23 copies · chains A
- ZN · Zinc ion · metal · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 894 | 0.74 | 0.78 | 74 | empty |
| 2 | 442 | 0.65 | 0.78 | 45 | empty |
| 3 | 298 | 0.59 | 0.78 | 36 | empty |
| 4 | 100 | 0.37 | 0.75 | 17 | empty |
| 5 | 66 | 0.35 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 965 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 glycan, 2 disulfide (N-glycosylation, disulfide).
Compared structures
- 4HOM · Crystal structure of porcine aminopeptidase-N complexed with substance P · the same entry in another collection · chain A against A, TM-score 1.00
- P15145 · AlphaFold monomer V2.0 prediction for aminopeptidase N (P15145) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 4HOM · PDBe 4HOM · UniProt P15145
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