3M6L

Crystal structure of transketolase in complex with thiamine diphosphate, ribose-5-phosphate and calcium ion


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.201
  • R-Value Work: 0.160

Literature

Macromolecules
Sequence Display for 3M6L

Classification: TRANSFERASE

Total Structure Weight: 71365.30

Macromolecule Entities
Molecule Chains Length Organism Details
Transketolase A 635 Campylobacter jejuni EC#: 2.2.1.1 IUBMB
Gene Name(s): tkt Cj1645
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
TPP
Query on TPP

A THIAMINE DIPHOSPHATE
C12 H19 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-O
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
R5P
Query on R5P

A RIBOSE-5-PHOSPHATE
C5 H11 O8 P
PPQRONHOSHZGFQ-LMVFSUKVSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

A PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
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)
EDO
Query on EDO

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

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-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 = 130.92 α = 90.00
b = 71.46 β = 109.48
c = 69.62 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-03-15
  • Released Date: 2010-04-28
  • Deposition author(s): Nocek, B., Makowska-Grzyska, M., Maltseva, N., Joachimiak, A., Anderson, W., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History

  • Version 1_0: 2010-04-28

    Type: Initial release

  • Version 1_1: 2011-07-13

    Type: Version format compliance

  • Version 1_2: 2014-10-01

    Type: Structure summary

  • Version 1_3: 2017-11-08

    Type: Advisory, Refinement description