3D6K

The crystal structure of a putative aminotransferase from Corynebacterium diphtheriae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.241
  • R-Value Work: 0.190

Literature

Macromolecules
Sequence Display for 3D6K

Classification: TRANSFERASE

Total Structure Weight: 187249.16

Macromolecule Entities
Molecule Chains Length Organism Details
Putative aminotransferase A, B, C, D 422 Corynebacterium diphtheriae Gene Name(s): DIP0257
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SO4
Query on SO4

A, B, C, D SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A, B, C, D 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A, B, C, D CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
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, B, C, D L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.241
  • R-Value Work: 0.190
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 89.25 α = 90.00
b = 56.08 β = 102.47
c = 173.59 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-05-19
  • Released Date: 2008-07-15
  • Deposition author(s): Tan, K., Zhang, R., Duggan, E., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History

  • Version 1_0: 2008-07-15

    Type: Initial release

  • Version 1_1: 2011-07-13

    Type: Advisory, Version format compliance