4DKJ

CpG specific methyltransferase in complex with target DNA

Structural Biology Knowledgebase: 4DKJ SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.216
  • R-Value Work: 0.176

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4DKJ

Classification: TRANSFERASE / DNA

Total Structure Weight: 56380.79


Macromolecule Entities
Molecule Chains Length Organism Details
Cytosine-specific methyltransferase A 403 Mycoplasma penetrans EC#: 2.1.1.37 IUBMB
Mutation: Q68R, K71R, S295P
Gene Name(s): MYPE4940
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*CP*CP*AP*CP*AP*TP*GP*(C37)P*GP*CP*TP*GP*AP*A)-3') B 14 synthetic
DNA (5'-D(*GP*TP*TP*CP*AP*GP*(5CM)P*GP*CP*AP*TP*GP*TP*G)-3') C 14 synthetic

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

A S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-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)
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
C37
Query on C37
B DNA LINKING C9 H13 F N3 O7 P DC
5CM
Query on 5CM
C DNA LINKING C10 H16 N3 O7 P DC

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.216
  • R-Value Work: 0.176
  • Space Group: P 41 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 83.95 α = 90.00
b = 83.95 β = 90.00
c = 173.84 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-02-03
  • Released Date: 2012-12-05
  • Deposition author(s): Wojciechowski, M., Czapinska, H., Bochtler, M.

Revision History

  • 2013-01-16
    Type: Citation | Details: Citation update
  • 2013-01-02
    Type: Citation | Details: Citation update
  • 2012-12-19
    Type: Citation | Details: citation update