1GP6

Anthocyanidin synthase from Arabidopsis thaliana complexed with trans-dihydroquercetin (with 30 min exposure to O2)

Structural Biology Knowledgebase: 1GP6 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.222
  • R-Value Work: 0.194

Literature

Macromolecules
Sequence Display for 1GP6

Classification: OXIDOREDUCTASE

Total Structure Weight: 41622.65

Macromolecule Entities
Molecule Chains Length Organism Details
LEUCOANTHOCYANIDIN DIOXYGENASE A 356 Arabidopsis thaliana EC#: 1.14.11.19 IUBMB
Gene Name(s): LDOX At4g22880 F7H19.60
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
DH2
Query on DH2

A (2S,3S)-2-(3,4-DIHYDROXYPHENYL)-3,5,7-TRIHYDROXY- 2,3-DIHYDRO-4H-CHROMEN-4-ONE
(2S,3S)-TRANS-DIHYDROQUERCETIN (Synonym)
C15 H12 O7
CXQWRCVTCMQVQX-CABCVRRESA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
QUE
Query on QUE

A 3,5,7,3',4'-PENTAHYDROXYFLAVONE
QUERCETIN (Synonym)
C15 H10 O7
REFJWTPEDVJJIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MES
Query on MES

A 2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SIN
Query on SIN

A SUCCINIC ACID
C4 H6 O4
KDYFGRWQOYBRFD-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FE2
Query on FE2

A FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.222
  • R-Value Work: 0.194
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 61.26 α = 90.00
b = 72.39 β = 90.00
c = 87.05 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-10-30
  • Released Date: 2002-02-21
  • Deposition author(s): Wilmouth, R.C., Turnbull, J.J., Welford, R.W.D., Clifton, I.J., Prescott, A.G., Schofield, C.J.

Revision History

  • 2013-09-04
    Type: Sequence database correspondence | Details: DBREF
  • 2013-09-04
    Type: Citation | Details: REMARK 1,JRNL
  • 2013-09-04
    Type: Entry authorship | Details: AUTHOR
  • 2013-09-04
    Type: Polymer description | Details: COMPND
  • 2013-09-04
    Type: Version format compliance | Details: REMARK 4
  • 2013-09-04
    Type: Biological assembly | Details: REMARK 300,REMARK 350
  • 2013-09-04
    Type: Atom nomenclature | Details: ATOM
  • 2013-09-04
    Type: Other | Details: REMARK 465,TER,REMARK 470,HEADER,REMARK 525,MASTER
  • 2013-09-04
    Type: Source and taxonomy | Details: SOURCE
  • 2013-09-04
    Type: Refinement description | Details: REMARK 3
  • 2013-09-04
    Type: Function and keywords | Details: KEYWDS
  • 2013-09-04
    Type: Geometry validation | Details: REMARK 500
  • 2013-09-04
    Type: Non-polymer description | Details: FORMUL
  • 2013-09-04
    Type: Data collection | Details: REMARK 200