1GP5

Anthocyanidin synthase from Arabidopsis thaliana complexed with trans-dihydroquercetin

Structural Biology Knowledgebase: 1GP5 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.237
  • R-Value Work: 0.204

Literature

Macromolecules
Sequence Display for 1GP5

Classification: OXIDOREDUCTASE

Total Structure Weight: 41652.68

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
DQH
Query on DQH

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

A 2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FE
Query on FE

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.237
  • R-Value Work: 0.204
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 62.03 α = 90.00
b = 74.36 β = 90.00
c = 88.11 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: Citation | Details: REMARK 1
  • 2013-09-04
    Type: Sequence database correspondence | Details: DBREF
  • 2013-09-04
    Type: Refinement description | Details: REMARK 3
  • 2013-09-04
    Type: Biological assembly | Details: REMARK 300,REMARK 350
  • 2013-09-04
    Type: Version format compliance | Details: REMARK 4