2IOD

Binding of two substrate analogue molecules to dihydroflavonol-4-reductase alters the functional geometry of the catalytic site

• PDB DOI: https://doi.org/10.2210/pdb2IOD/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Vitis vinifera
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-10-10 Released: 2007-09-11 
• Deposition Author(s): Petit, P., Langlois d'Estaintot, B., Granier, T., Gallois, B.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free: 0.257 
• R-Value Work: 0.189 
• R-Value Observed: 0.193 

Starting Model: experimental

Literature

Binding of two substrate analogue molecules to dihydroflavonol-4-reductase alters the functional geometry of the catalytic site

Petit, P., Langlois d'Estaintot, B., Granier, T., Gallois, B.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 156.3 kDa 
• Atom Count: 11,125 
• Modelled Residue Count: 1,292 
• Deposited Residue Count: 1,348 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydroflavonol 4-reductase	A, B, C, D	337	Vitis vinifera	Mutation(s): 0  Gene Names: dfr1 EC: 1.1.1.219 (PDB Primary Data), 1.1.1.234 (UniProt)
UniProt
Find proteins for P51110 (Vitis vinifera) Explore P51110  Go to UniProtKB:  P51110

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	E [auth A], H [auth B], K [auth C], N [auth D]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
MYC	F [auth A], G [auth A], I [auth B], J [auth B], L [auth C], M [auth C], O [auth D], P [auth D]	3,5,7-TRIHYDROXY-2-(3,4,5-TRIHYDROXYPHENYL)-4H-CHROMEN-4-ONE C15 H10 O8 IKMDFBPHZNJCSN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free: 0.257 
• R-Value Work: 0.189 
• R-Value Observed: 0.193 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.231	α = 90
b = 177.958	β = 104.77
c = 92.597	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
AMoRE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ProDC	data collection
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-09-11 
Deposition Author(s): Petit, P., Langlois d'Estaintot, B., Granier, T., Gallois, B.

Revision History  

• Version 1.0: 2007-09-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description