1GT8

DIHYDROPYRIMIDINE DEHYDROGENASE (DPD) FROM PIG, TERNARY COMPLEX WITH NADPH AND URACIL-4-ACETIC ACID

Structural Biology Knowledgebase: 1GT8 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.269
  • R-Value Work: 0.214

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1GT8

Classification: OXIDOREDUCTASE

Total Structure Weight: 460671.87

Macromolecule Entities
Molecule Chains Length Organism Details
DIHYDROPYRIMIDINE DEHYDROGENASE A, B, C, D 1025 Sus scrofa EC#: 1.3.1.2 IUBMB
Mutation: G60D
Gene Name(s): DPYD Gene View

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

A, B, C, D FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NDP
Query on NDP

A, B, C, D NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FMN
Query on FMN

A, B, C, D FLAVIN MONONUCLEOTIDE
RIBOFLAVIN MONOPHOSPHATE (Synonym)
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SF4
Query on SF4

A, B, C, D IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
UAA
Query on UAA

A, B, C, D URACIL-6-ACETIC ACID
6-CARBOXYMETHYLURACIL (Synonym)
C6 H6 N2 O4
NQAUNZZEYKWTHM-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.269
  • R-Value Work: 0.214
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 82.03 α = 90.00
b = 159.53 β = 97.16
c = 166.02 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-01-14
  • Released Date: 2002-04-11
  • Deposition author(s): Dobritzsch, D., Ricagno, S., Schneider, G., Schnackerz, K.D., Lindqvist, Y.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4