2IOD | pdb_00002iod

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 (Depositor), 0.261 (DCC)
R-Value Work:
0.189 (Depositor), 0.195 (DCC)
R-Value Observed:
0.193 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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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.

Macromolecule Content

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

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P51110
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download:Ideal Coordinates CCD File SDF format, chain N [auth D] SDF format, chain K [auth C] SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain N [auth D] MOL2 format, chain K [auth C] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain N [auth D] mmCIF format, chain K [auth C] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	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		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D]
MYC Query on MYC Download:Ideal Coordinates CCD File SDF format, chain P [auth D] SDF format, chain O [auth D] SDF format, chain M [auth C] SDF format, chain L [auth C] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain P [auth D] MOL2 format, chain O [auth D] MOL2 format, chain M [auth C] MOL2 format, chain L [auth C] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain P [auth D] mmCIF format, chain O [auth D] mmCIF format, chain M [auth C] mmCIF format, chain L [auth C] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A] G [auth A] I [auth B] J [auth B] L [auth C] 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		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain O [auth D] Focus chain P [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain O [auth D] Focus chain P [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.06 Å
R-Value Free: 0.257 (Depositor), 0.261 (DCC)
R-Value Work: 0.189 (Depositor), 0.195 (DCC)
R-Value Observed: 0.193 (Depositor)

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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2007-09-11

Deposition Author(s):

Petit, P.

Langlois d'Estaintot, B.

Granier, T.

Gallois, B.

Revision History (Full details and data files)

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

2IOD | pdb_00002iod

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

Literature

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

Biological Assembly 1

Biological Assembly 2

Biological Assembly 3

Biological Assembly 4

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Entry History

Deposition Data

Revision History (Full details and data files)