4R85

Crystal structure of 5-methylcytosine deaminase from Klebsiella pneumoniae liganded with 5-methylcytosine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.187
  • R-Value Work: 0.159

Literature

Macromolecules
Sequence Display for 4R85

Classification: HYDROLASE

Total Structure Weight: 291148.25

Macromolecule Entities
Molecule Chains Length Organism Details
Cytosine deaminase A, B, C..., D, E, FA, B, C, D, E, F 431 Klebsiella pneumoniae EC#: 3.5.4.1 IUBMB
Gene Name(s): KPNJ1_03949
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
17E
Query on 17E

A, B, C, D, E, F 5-methylcytosine
4-amino-5-methylpyrimidin-2(1H)-one (Synonym)
C5 H7 N3 O
LRSASMSXMSNRBT-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, B, C, D, E, F GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FE2
Query on FE2

A, B, C, D, E, F FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.187
  • R-Value Work: 0.159
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 111.48 α = 90.00
b = 137.67 β = 118.03
c = 112.09 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2014-08-29
  • Released Date: 2014-09-17
  • Deposition author(s): Fedorov, A.A., Fedorov, E.V., Hitchcock, D.S., Raushel, F.M., Almo, S.C.
  • Previous versions: 4JNP

Revision History

No revisions since initial release