5EPE

Crystal structure of SAM-dependent methyltransferase from Thiobacillus denitrificans in complex with S-Adenosyl-L-homocysteine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.167
  • R-Value Work: 0.136

Literature

Macromolecules
Sequence Display for 5EPE

Classification: TRANSFERASE

Total Structure Weight: 27854.63

Macromolecule Entities
Molecule Chains Length Organism Details
SAM-dependent methyltransferase A 248 Thiobacillus denitrificans EC#: 2.1.1 IUBMB
Gene Name(s): Tbd_1076
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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 NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

Unit Cell:

Length (Å) Angle (°)
a = 157.54 α = 90.00
b = 157.54 β = 90.00
c = 157.54 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2015-11-11
  • Released Date: 2015-11-25
  • Deposition author(s): LaRowe, C., Shabalin, I.G., Kutner, J., Handing, K.B., Stead, M., Hillerich, B.S., Ahmed, M., Seidel, R., Bonanno, J., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)

Revision History

  • Version 1_0: 2015-11-25

    Type: Initial release

  • Version 1_1: 2015-12-23

    Type: Other

  • Version 1_2: 2016-02-24

    Type: Other

  • Version 1_3: 2017-09-27

    Type: Author supporting evidence, Derived calculations, Refinement description