Research workbench
Human monoamine oxidase B in complex with lauryldimethylamine-N-oxide (ldao)
Analyse Human monoamine oxidase B in complex with lauryldimethylamine-N-oxide (ldao) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1OJD
- Type
- protein
- Length
- 4,964 residues
- Chains
- 10
- 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
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F, I, L | Amine oxidase [flavin-containing] B (EC 1.4.3.4) | protein | 497 | 39% helix, 20% strand | P27338 |
| B, D, G | Amine oxidase [flavin-containing] B (EC 1.4.3.4) | protein | 494 | 38% helix, 20% strand | P27338 |
| C, E, H | Amine oxidase [flavin-containing] B (EC 1.4.3.4) | protein | 498 | 39% helix, 20% strand | P27338 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 10 copies · chains A, B, C, D, E, F, G, H, I, L
- LDA · Lauryl dimethylamine-N-oxide · additive · 10 copies · chains A, B, C, D, E, F, G, H, I, L
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 | 495 | 0.89 | 0.95 | 71 | FAD, LDA |
| 2 | 499 | 0.88 | 0.95 | 73 | FAD, LDA |
| 3 | 494 | 0.88 | 0.95 | 71 | FAD, LDA |
| 4 | 480 | 0.88 | 0.95 | 69 | FAD, LDA |
| 5 | 474 | 0.88 | 0.95 | 70 | FAD, LDA |
Interfaces
10 interfaces between chains.
- G–H · 2125 Ų buried · 38 hydrogen bonds · protein-protein
- C–D · 2123 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 2119 Ų buried · 38 hydrogen bonds · protein-protein
- I–L · 2117 Ų buried · 40 hydrogen bonds · protein-protein
- E–F · 2100 Ų buried · 38 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 cofactor (flavinylation).
Compared structures
- 1OJD · HUMAN MONOAMINE OXIDASE B IN COMPLEX WITH Lauryldimethylamine-N-oxide (LDAO) · the same entry in another collection · chain L against L, 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 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 P27338
- Elsewhere: RCSB PDB 1OJD · PDBe 1OJD · UniProt P27338
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