Research workbench
Structure of berberine bridge enzyme, H174A variant in complex with (S)-reticuline
Analyse Structure of berberine bridge enzyme, H174A variant in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EC3
- Type
- protein
- Length
- 500 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, REN, NAG, MAN, BMA, CL
- Pockets
- 2 · best druggability 0.84
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 | 500 | 39% helix, 21% strand | P30986 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- REN · (S)-reticuline · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 3 copies
- BMA · beta-D-mannopyranose · sugar
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 715 | 0.84 | 0.88 | 86 | FAD, REN |
| 2 | 93 | 0.36 | 0.75 | 19 | empty |
Modifications
Observed in the structure: 2 cofactor, 2 glycan, 1 disulfide (flavinylation, N-glycosylation, disulfide).
Compared structures
- 4EC3 · Structure of berberine bridge enzyme, H174A variant in complex with (S)-reticuline · the same entry in another collection · chain A against A, TM-score 1.00
- P30986 · AlphaFold monomer V2.0 prediction for reticuline oxidase (P30986) · a predicted model of the same protein · chain A 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 P30986
- Elsewhere: RCSB PDB 4EC3 · PDBe 4EC3 · UniProt P30986
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