MolNFT v1 · #56140 · protein
Crystal structure of human monoamine oxidase a with harmine
2Z5X · Amine oxidase [flavin-containing] a: “Crystal structure of human monoamine oxidase a with harmine”. X-ray diffraction, 3 ligands (DCX, FAD, HRM), 5 pockets (best druggability 0.85). MolNFT v1 #56140 on GenesisL1: 3D structure…
- PDB
- 2Z5X
- Type
- protein
- Length
- 513 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amine oxidase [flavin-containing] a
- EC
- 1.4.3.4
- UniProt
- P21397
- Ligands
- DCX, FAD, HRM
- Pockets
- 5 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Amine oxidase [flavin-containing] a (EC 1.4.3.4) | protein | 513 | 41% helix, 19% strand | P21397 |
Ligands and binding sites
- DCX · Decyl(dimethyl)phosphine oxide · ligand · 2 copies · chains A
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- HRM · 7-methoxy-1-methyl-9H-beta-carboline · ligand · chains A
- GOL · Glycerol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 463 | 0.85 | 0.92 | 73 | FAD, HRM |
| 2 | 50 | 0.69 | 0.97 | 22 | empty |
| 3 | 188 | 0.54 | 0.79 | 28 | empty |
| 4 | 138 | 0.50 | 0.79 | 22 | empty |
| 5 | 83 | 0.43 | 0.79 | 18 | empty |
Modifications
Observed in the structure: 1 cofactor (flavinylation).
Compared structures
- 2Z5X · Crystal Structure of Human Monoamine Oxidase A with Harmine · the same entry in another collection · chain A against A, TM-score 1.00
- P21397 · AlphaFold monomer V2.0 prediction for amine oxidase [flavin- containing] a (P21397) · 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 P21397
- Elsewhere: RCSB PDB 2Z5X · PDBe 2Z5X · UniProt P21397
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