Research workbench
Rasagiline-inhibited human monoamine oxidase B in complex with 2-(2- benzofuranyl)-2-imidazoline
Analyse Rasagiline-inhibited human monoamine oxidase B in complex with 2-(2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XFQ
- 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, RAS, XCG, C15
- Pockets
- 11 · best druggability 0.87
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, 21% strand | P27338 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- RAS · (1R)-N-(prop-2-en-1-yl)-2,3-dihydro-1H-inden-1-amine · ligand · 2 copies · chains A, B
- XCG · 2-(2-benzofuranyl)-2-imidazoline · ligand · 2 copies · chains A, B
- C15 · N-dodecyl-N,N-dimethyl-3-ammonio-1-propanesulfonate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 490 | 0.87 | 0.94 | 73 | FAD, RAS, XCG |
| 2 | 378 | 0.87 | 0.95 | 56 | FAD, RAS |
| 3 | 369 | 0.69 | 0.81 | 46 | XCG |
| 4 | 342 | 0.59 | 0.77 | 45 | empty |
| 5 | 231 | 0.55 | 0.77 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 2132 Ų buried · 37 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (flavinylation).
Compared structures
- 2XFQ · Rasagiline-inhibited human monoamine oxidase B in complex with 2-(2… · 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 2XFQ · PDBe 2XFQ · UniProt P27338
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