Research workbench
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 v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- 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 · 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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