MolNFT v1 · #66167 · protein
Crystal structure of human diamine oxidase in complex with the inhibitor berenil
3HIG · Amiloride-sensitive amine oxidase: “Crystal structure of human diamine oxidase in complex with the inhibitor berenil”. X-ray diffraction, 5 ligands (BRN, NAG, BMA), 20 pockets (best druggability 0.87). MolNFT v1 #66167 on GenesisL1…
- PDB
- 3HIG
- 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
- BRN, NAG, BMA, CA, CU
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Amiloride-sensitive amine oxidase (EC 1.4.3.22) | protein | 715 | 16% helix, 39% strand | P19801 |
| B | Amiloride-sensitive amine oxidase (EC 1.4.3.22) | protein | 710 | 16% helix, 40% strand | P19801 |
Ligands and binding sites
- BRN · Berenil · 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1100 | 0.87 | 0.88 | 109 | empty |
| 2 | 174 | 0.78 | 0.94 | 29 | empty |
| 3 | 551 | 0.78 | 0.84 | 59 | BRN |
| 4 | 489 | 0.77 | 0.85 | 56 | BRN |
| 5 | 196 | 0.75 | 0.91 | 37 | empty |
Interfaces
1 interface between chains.
- A–B · 8737 Ų buried · 139 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 glycan, 5 disulfide, 2 modified (N-glycosylation, disulfide, nonstandard).
Compared structures
- 3HIG · Crystal structure of human diamine oxidase in complex with the inhibitor berenil · 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 3HIG · PDBe 3HIG · UniProt P19801
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