Research workbench
Crystal structure of human diamine oxidase in space group C2221
Analyse Crystal structure of human diamine oxidase in space group C2221 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3K5T
- Type
- protein
- Length
- 712 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diamine oxidase
- EC
- 1.4.3.22
- UniProt
- P19801
- Ligands
- NAG, CA, CU
- Pockets
- 7 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 15% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Diamine oxidase (EC 1.4.3.22) | protein | 712 | 15% helix, 38% strand | P19801 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A
- CA · Calcium ion · metal · 2 copies · chains A
- CU · Copper (II) ion · metal · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 476 | 0.70 | 0.80 | 44 | empty |
| 2 | 353 | 0.59 | 0.76 | 33 | empty |
| 3 | 271 | 0.57 | 0.78 | 28 | empty |
| 4 | 97 | 0.43 | 0.78 | 18 | empty |
| 5 | 92 | 0.39 | 0.76 | 15 | empty |
Modifications
Observed in the structure: 3 glycan, 1 disulfide, 1 modified (N-glycosylation, disulfide, nonstandard).
Compared structures
- 3K5T · Crystal structure of human diamine oxidase in space group C2221 · 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 3K5T · PDBe 3K5T · UniProt P19801
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