1RAK

Bacterial cytosine deaminase D314S mutant bound to 5-fluoro-4-(S)-hydroxyl-3,4-dihydropyrimidine.

Structural Biology Knowledgebase: 1RAK SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.32 Å
  • R-Value Free: 0.179
  • R-Value Work: 0.172

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1RAK

Classification: HYDROLASE

Total Structure Weight: 48112.55

Macromolecule Entities
Molecule Chains Length Organism Details
Cytosine deaminase A 430 Escherichia coli EC#: 3.5.4.1 IUBMB
Mutation: S1A, D314S
Gene Name(s): codA b0337 JW0328
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A (4S)-5-FLUORO-4-HYDROXY-3,4-DIHYDROPYRIMIDIN- 2(1H)-ONE
4-DIHYDROPYRIMIDINE, (Synonym)
C4 H5 F N2 O2
PRVUBDAKZJCBTI-VKHMYHEASA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FE
Query on FE

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.32 Å
  • R-Value Free: 0.179
  • R-Value Work: 0.172
  • Space Group: H 3 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 109.48 α = 90.00
b = 109.48 β = 90.00
c = 241.09 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-10-31
  • Released Date: 2004-10-05
  • Deposition author(s): Mahan, S.D., Ireton, G.C., Stoddard, B.L., Black, M.E.

Revision History

  • 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