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Structure of berberine bridge enzyme from eschscholzia californica, monoclinic crystal form
Analyse Structure of berberine bridge enzyme from eschscholzia californica, monoclinic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3D2H
- Type
- protein
- Length
- 498 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Berberine bridge-forming enzyme
- EC
- 1.21.3.3
- UniProt
- P30986
- Ligands
- FAD, FSH, MAN, NAG
- 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 | Berberine bridge-forming enzyme (EC 1.21.3.3) | protein | 498 | 39% helix, 21% strand | P30986 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- FSH · (2R,3S,4S)-5-[(4R)-6',7'-dimethyl-2,3',5-trioxo-1'H-spiro[imidazolidine-4,2'-quinoxalin]-4'(3'H)-yl]-2,3,4-trihydroxypentyl-adenosine diphosphate · ligand · chains A
- MAN · alpha-D-mannopyranose · sugar · 4 copies
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · 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 | 839 | 0.86 | 0.88 | 95 | FAD, FSH |
| 2 | 74 | 0.32 | 0.74 | 19 | empty |
| 3 | 63 | 0.29 | 0.74 | 16 | empty |
Modifications
Observed in the structure: 2 cofactor, 2 covalent, 2 glycan, 1 disulfide (flavinylation, covalent ligand, N-glycosylation, disulfide).
Compared structures
- 3D2H · Structure of berberine bridge enzyme from Eschscholzia californica, monoclinic crystal… · 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 3D2H · PDBe 3D2H · UniProt P30986
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