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Crystal structure of human diamine oxidase in complex with the inhibitor pentamidine
Analyse Crystal structure of human diamine oxidase in complex with the inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HII
- Type
- protein
- Length
- 1,425 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.149
- Source
- Homo sapiens
- Molecule
- Amiloride-sensitive amine oxidase
- EC
- 1.4.3.22
- UniProt
- P19801
- Ligands
- PNT, NAG, BMA, CA, CU
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · resolution 2.149 · 2 distinct chains · 17% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Amiloride-sensitive amine oxidase (EC 1.4.3.22) | protein | 715 | 17% helix, 40% strand | P19801 |
| B | Amiloride-sensitive amine oxidase (EC 1.4.3.22) | protein | 710 | 17% helix, 40% strand | P19801 |
Ligands and binding sites
- PNT · 1,5-bis(4-amidinophenoxy)pentane · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar
- CA · Calcium ion · metal · 4 copies · chains A, B
- CU · Copper (II) ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1195 | 0.86 | 0.87 | 109 | empty |
| 2 | 625 | 0.77 | 0.83 | 56 | PNT |
| 3 | 161 | 0.77 | 0.94 | 29 | empty |
| 4 | 543 | 0.77 | 0.84 | 51 | PNT |
| 5 | 182 | 0.75 | 0.91 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 8751 Ų buried · 139 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 glycan, 5 disulfide, 2 modified (N-glycosylation, disulfide, nonstandard).
Compared structures
- 3HII · Crystal structure of human diamine oxidase in complex with the inhibitor pentamidine · the same entry in another collection · chain A against A, TM-score 1.00
- P19801 · AlphaFold monomer V2.0 prediction for amiloride-sensitive amine oxidase… · a predicted model of the same protein · chain A against A, TM-score 1.00
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 P19801
- Elsewhere: RCSB PDB 3HII · PDBe 3HII · UniProt P19801
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