1TV5

Plasmodium falciparum dihydroorotate dehydrogenase with a bound inhibitor

Structural Biology Knowledgebase: 1TV5 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.243
  • R-Value Work: 0.201

Literature

Macromolecules
Sequence Display for 1TV5

Classification: OXIDOREDUCTASE

Total Structure Weight: 51940.43

Macromolecule Entities
Molecule Chains Length Organism Details
Dihydroorotate dehydrogenase homolog, mitochondrial A 443 Plasmodium falciparum EC#: 1.3.5.2 IUBMB
Fragment: Fully functional N-terminal deletion mutant
Gene Name(s): PFF0160c
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A FLAVIN MONONUCLEOTIDE
RIBOFLAVIN MONOPHOSPHATE (Synonym)
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
N8E
Query on N8E

A 3,6,9,12,15-PENTAOXATRICOSAN-1-OL
N-OCTYLPENTAOXYETHYLENE; PENTAETHYLENE GLYCOL MONOOCTYL ETHER; OCTYLPENTAGLYCOL N- OCTYLPENTAOXYETHYLENE (Synonym)
C18 H38 O6
MJELOWOAIAAUJT-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
A26
Query on A26

A (2Z)-2-cyano-3-hydroxy-N-[4-(trifluoromethyl)phenyl]but- 2-enamide
ANTIPROLIFERATIVE AGENT A771726 (Synonym)
C12 H9 F3 N2 O2
UTNUDOFZCWSZMS-YFHOEESVSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ORO
Query on ORO

A OROTIC ACID
C5 H4 N2 O4
PXQPEWDEAKTCGB-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
A26 IC50: 11390 - 190100 nM (100) BindingDB
Ki: 22000 - 23350 nM (100) BindingDB

Ki: 1000 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.243
  • R-Value Work: 0.201
  • Space Group: H 3 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 105.43 α = 90.00
b = 105.43 β = 90.00
c = 276.63 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-06-27
  • Released Date: 2005-09-06
  • Deposition author(s): Hurt, D.E., Widom, J., Clardy, J.

Revision History

  • 2012-07-18
    Type: Non-polymer description | Details: --
  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4