1GTH

DIHYDROPYRIMIDINE DEHYDROGENASE (DPD) FROM PIG, TERNARY COMPLEX WITH NADPH AND 5-IODOURACIL

Structural Biology Knowledgebase: 1GTH SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.209
  • R-Value Work: 0.177

Literature

Macromolecules
Sequence Display for 1GTH

Classification: OXIDOREDUCTASE

Total Structure Weight: 460821.66

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
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 7 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 NGL
 
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 NGL
 
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 NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SF4
Query on SF4

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

A, B (5S)-5-IODODIHYDRO-2,4(1H,3H)-PYRIMIDINEDIONE
C4 H5 I N2 O2
YGKCTZPSAOUUMT-REOHCLBHSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
IUR
Query on IUR

C 5-IODOURACIL
C4 H3 I N2 O2
KSNXJLQDQOIRIP-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
URA
Query on URA

D URACIL
C4 H4 N2 O2
ISAKRJDGNUQOIC-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
IUR IC50: 220 nM (92) BindingDB

N/A in BindingMoad
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.209
  • R-Value Work: 0.177
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 82.21 α = 90.00
b = 159.69 β = 97.11
c = 167.59 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-01-15
  • 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