Research workbench
Structure of berberine bridge enzyme in complex with (S)-scoulerine
Analyse Structure of berberine bridge enzyme in complex with (S)-scoulerine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FW9
- Type
- protein
- Length
- 495 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reticuline oxidase
- EC
- 1.21.3.3
- UniProt
- P30986
- Ligands
- FAD, SLX, NAG, MAN, MG
- Pockets
- 3 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reticuline oxidase (EC 1.21.3.3) | protein | 495 | 39% helix, 21% strand | P30986 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- SLX · (13aS)-3,10-dimethoxy-5,8,13,13a-tetrahydro-6H-isoquino[3,2-a]isoquinoline-2,9-diol · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
- MAN · alpha-D-mannopyranose · sugar
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 685 | 0.86 | 0.90 | 81 | FAD, SLX |
| 2 | 98 | 0.35 | 0.74 | 17 | empty |
| 3 | 57 | 0.33 | 0.78 | 15 | empty |
Modifications
Observed in the structure: 2 cofactor, 2 glycan, 1 disulfide (flavinylation, N-glycosylation, disulfide).
Compared structures
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 P30986
- Elsewhere: RCSB PDB 3FW9 · PDBe 3FW9 · UniProt P30986
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