Research workbench
Crystal structure of human monoamine oxidase B in complex with methylene blue and bearing the double mutation I199A- Y326A
Analyse Crystal structure of human monoamine oxidase B in complex with methylene blue… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZYX
- Type
- protein
- Length
- 993 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amine oxidase [flavin-containing] B
- EC
- 1.4.3.4
- UniProt
- P27338
- Ligands
- FAD, MBT
- Pockets
- 10 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Amine oxidase [flavin-containing] B (EC 1.4.3.4) | protein | 499 | 38% helix, 19% strand | P27338 |
| B | Amine oxidase [flavin-containing] B (EC 1.4.3.4) | protein | 494 | 38% helix, 20% strand | P27338 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- MBT · 3,7-bis(dimethylamino)phenothiazin-5-ium · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 883 | 0.86 | 0.88 | 103 | FAD, MBT |
| 2 | 869 | 0.86 | 0.88 | 102 | FAD, MBT |
| 3 | 230 | 0.57 | 0.79 | 34 | empty |
| 4 | 221 | 0.53 | 0.77 | 32 | empty |
| 5 | 94 | 0.39 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 2147 Ų buried · 40 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (flavinylation).
Compared structures
- 3ZYX · Crystal structure of human monoamine oxidase B in complex with methylene blue and bearing… · the same entry in another collection · chain A against A, TM-score 1.00
- P27338 · AlphaFold monomer V2.0 prediction for amine oxidase [flavin- containing] B (P27338) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P27338
- Elsewhere: RCSB PDB 3ZYX · PDBe 3ZYX · UniProt P27338
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