2NNL | pdb_00002nnl

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/pdb2NNL/pdb

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


• Deposited: 2006-10-24 Released: 2007-11-13 
• Deposition Author(s): Petit, P., Langlois D'Estaintot, B., Granier, T., Gallois, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.242 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

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.

Macromolecule Content 

• Total Structure Weight: 77.45 kDa 
• Atom Count: 5,723 
• Modeled Residue Count: 650 
• Deposited Residue Count: 674 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydroflavonol 4-reductase	A [auth D], B [auth F]	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	C [auth D], E [auth F]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
ERD	D, F	(2S)-2-(3,4-DIHYDROXYPHENYL)-5,7-DIHYDROXY-2,3-DIHYDRO-4H-CHROMEN-4-ONE C15 H12 O6 SBHXYTNGIZCORC-ZDUSSCGKSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.242 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.825	α = 90
b = 90.143	β = 90
c = 93.297	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-11-13 
Deposition Author(s): Petit, P., Langlois D'Estaintot, B., Granier, T., Gallois, B.

Revision History  

• Version 1.0: 2007-11-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2019-12-25
  Changes: Data collection
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description