MolNFT v1 · #52125 · protein
Structure of human mao B in complex with benzylhydrazine
2VRL · Amine oxidase [flavin-containing] B: “Structure of human mao B in complex with benzylhydrazine”. X-ray diffraction, 2 ligands (FAD, MBN), 14 pockets (best druggability 0.88). MolNFT v1 #52125 on GenesisL1: 3D structure, binding…
- PDB
- 2VRL
- 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, MBN
- Pockets
- 14 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 19% 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, 19% strand | P27338 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- MBN · Toluene · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 468 | 0.88 | 0.95 | 71 | FAD, MBN |
| 2 | 482 | 0.88 | 0.95 | 69 | FAD, MBN |
| 3 | 54 | 0.59 | 0.91 | 22 | empty |
| 4 | 290 | 0.57 | 0.77 | 40 | empty |
| 5 | 256 | 0.57 | 0.78 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 2128 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (flavinylation).
Compared structures
- 2VRL · Structure of human MAO B in complex with benzylhydrazine · 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 2VRL · PDBe 2VRL · UniProt P27338
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