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The structure of mao-N-D3, a variant of monoamine oxidase from aspergillus niger.
Analyse The structure of mao-N-D3, a variant of monoamine oxidase from aspergillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VVL
- Type
- protein
- Length
- 3,820 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Monoamine oxidase N
- EC
- 1.4.3.4
- UniProt
- P46882
- Ligands
- FAD
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 8 distinct chains · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Monoamine oxidase N (EC 1.4.3.4) | protein | 478 | 34% helix, 23% strand | P46882 |
| B | Monoamine oxidase N (EC 1.4.3.4) | protein | 476 | 33% helix, 22% strand | P46882 |
| C | Monoamine oxidase N (EC 1.4.3.4) | protein | 477 | 32% helix, 23% strand | P46882 |
| D | Monoamine oxidase N (EC 1.4.3.4) | protein | 478 | 34% helix, 24% strand | P46882 |
| E | Monoamine oxidase N (EC 1.4.3.4) | protein | 477 | 34% helix, 25% strand | P46882 |
| F | Monoamine oxidase N (EC 1.4.3.4) | protein | 478 | 33% helix, 22% strand | P46882 |
| G | Monoamine oxidase N (EC 1.4.3.4) | protein | 478 | 34% helix, 25% strand | P46882 |
| H | Monoamine oxidase N (EC 1.4.3.4) | protein | 478 | 35% helix, 23% strand | P46882 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, E, C, B, D, H, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 380 | 0.87 | 0.96 | 56 | FAD |
| 2 | 382 | 0.87 | 0.96 | 56 | FAD |
| 3 | 400 | 0.87 | 0.95 | 58 | FAD |
| 4 | 387 | 0.87 | 0.95 | 59 | FAD |
| 5 | 383 | 0.87 | 0.95 | 57 | FAD |
Interfaces
11 interfaces between chains.
- D–H · 1774 Ų buried · 20 hydrogen bonds · protein-protein
- A–E · 1714 Ų buried · 17 hydrogen bonds · protein-protein
- F–G · 1712 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1710 Ų buried · 16 hydrogen bonds · protein-protein
- B–F · 417 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 2VVL · The structure of MAO-N-D3, a variant of monoamine oxidase from Aspergillus niger. · the same entry in another collection · chain H against H, TM-score 1.00
- P46882 · AlphaFold monomer V2.0 prediction for monoamine oxidase N (P46882) · a predicted model of the same protein · chain G 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 P46882
- Elsewhere: RCSB PDB 2VVL · PDBe 2VVL · UniProt P46882
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