1G55

Structure of human DNMT2, an enigmatic DNA methyltransferase homologue

Structural Biology Knowledgebase: 1G55 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.250
  • R-Value Work: 0.210

Literature

Macromolecules
Sequence Display for 1G55

Classification: TRANSFERASE

Total Structure Weight: 39927.45

Macromolecule Entities
Molecule Chains Length Organism Details
DNA CYTOSINE METHYLTRANSFERASE DNMT2 A 343 Homo sapiens EC#: 2.1.1.37 IUBMB
Mutation: ΔS191, ΔV192, ΔH193, ΔP194, ΔQ195, ΔK196, ΔY197, ΔA198, ΔM199, ΔD200, ΔV201, ΔE202, ΔN203, ΔK204, ΔI205, ΔQ206, ΔE207, ΔK208, ΔN209, ΔV210, ΔE211, ΔP212, ΔN213, ΔI214, ΔS215, ΔF216, ΔD217, ΔG218, ΔS219, ΔI220, ΔQ221, ΔC222, ΔS223, ΔG224, ΔK225, ΔD226, ΔA227, ΔI228, ΔL229, ΔF230, ΔK231, ΔL232, ΔE233, ΔT234, ΔA235, ΔE236, ΔE237
Gene Name(s): TRDMT1 Gene View DNMT2
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 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 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)
GOL
Query on GOL

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

A BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
CSO
Query on CSO
A L-PEPTIDE LINKING C3 H7 N O3 S CYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.250
  • R-Value Work: 0.210
  • Space Group: I 41

Unit Cell:

Length (Å) Angle (°)
a = 116.50 α = 90.00
b = 116.50 β = 90.00
c = 69.80 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2000-10-30
  • Released Date: 2001-01-17
  • Deposition author(s): Dong, A., Yoder, J.A., Zhang, X., Zhou, L., Bestor, T.H., Cheng, X.

Revision History

  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4