Download MendeleyStructural roles of biocovalent flaninylation in berberine bridge enzyme
Winkler, A., Motz, K., Riedl, S., Puhl, M., Macheroux, P., Gruber, K.To be published.
3FW9
Structure of berberine bridge enzyme in complex with (S)-scoulerine
- PDB DOI: https://doi.org/10.2210/pdb3FW9/pdb
- Classification: FLAVOPROTEIN
- Organism(s): Eschscholzia californica
- Expression System: Komagataella pastoris
- Mutation(s): No
- Deposited: 2009-01-17 Released: 2009-05-19
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.49 Å
- R-Value Free: 0.195
- R-Value Work: 0.172
- R-Value Observed: 0.173
This is version 2.1 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Reticuline oxidase | 495 | Eschscholzia californica | Mutation(s): 0 Gene Names: BBE1 EC: 1.21.3.3 |  | |
UniProt | |||||
Find proteins for P30986 (Eschscholzia californica) Explore P30986 Go to UniProtKB: P30986 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P30986 | ||||
Protein Feature ViewExpand | |||||
| |||||
Oligosaccharides
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Chain Length | 2D Diagram | Glycosylation | 3D Interactions |
| alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | B | 3 |  | N-Glycosylation | Oligosaccharides Interaction |
Glycosylation Resources | |||||
GlyTouCan: G62182OO GlyCosmos: G62182OO GlyGen: G62182OO | |||||
Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| FAD Query on FAD | C [auth A] | FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N |  | Ligand Interaction | |
| SLX Query on SLX | D [auth A] | (13aS)-3,10-dimethoxy-5,8,13,13a-tetrahydro-6H-isoquino[3,2-a]isoquinoline-2,9-diol C19 H21 N O4 KNWVMRVOBAFFMH-HNNXBMFYSA-N |  | Ligand Interaction | |
| NAG Query on NAG | E [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | Ligand Interaction | |
| MG Query on MG | F [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | Ligand Interaction | |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.49 Å
- R-Value Free: 0.195
- R-Value Work: 0.172
- R-Value Observed: 0.173
- Space Group: P 41 21 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 68.72 | α = 90 |
| b = 68.72 | β = 90 |
| c = 247.17 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| MAR345dtb | data collection |
| XDS | data reduction |
| XSCALE | data scaling |
| PHASER | phasing |
Entry History
Deposition Data
- Released Date: 2009-05-19 Deposition Author(s): Winkler, A., Macheroux, P., Gruber, K.
Revision History (Full details and data files)
- Version 1.0: 2009-05-19
Type: Initial release - Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2023-09-06
Changes: Data collection, Database references, Refinement description, Structure summary
