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Structure of berberine bridge enzyme in complex with (S)-reticuline

Analyse Structure of berberine bridge enzyme in complex with (S)-reticuline in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3D2D
Type: protein
Length: 500 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, REN, MAN, NAG
Pockets: 2 · best druggability 0.85

Structure

x-ray diffraction · 1 distinct chain · 37% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Berberine bridge-forming enzyme (EC 1.21.3.3)	protein	500	37% helix, 21% strand	P30986

Ligands and binding sites

FAD · Flavin-adenine dinucleotide · ligand · chains A
REN · (S)-reticuline · 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

2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	717	0.85	0.89	89	FAD, REN
2	166	0.45	0.75	37	empty

Modifications

Observed in the structure: 2 cofactor, 2 glycan, 1 disulfide (flavinylation, N-glycosylation, disulfide).

Compared structures

3D2D · Structure of berberine bridge enzyme 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 3D2D · PDBe 3D2D · UniProt P30986

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