4YDU

Crystal structure of E. coli YgjD-YeaZ heterodimer in complex with ADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.253
  • R-Value Work: 0.202

Literature

Macromolecules
Sequence Display for 4YDU

Classification: transferase

Total Structure Weight: 128462.42

Macromolecule Entities
Molecule Chains Length Organism Details
tRNA N6-adenosine threonylcarbamoyltransferase A, B 343 Escherichia coli EC#: 2.3.1.234 IUBMB
Gene Name(s): tsaD gcp ygjD b3064 JW3036
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
tRNA threonylcarbamoyladenosine biosynthesis protein TsaB C, D 237 Escherichia coli Gene Name(s): tsaB yeaZ b1807 JW1796
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ADP
Query on ADP

A, B, C, D ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACT
Query on ACT

A, B, C, D ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FE
Query on FE

A, B FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.253
  • R-Value Work: 0.202
  • Space Group: P 1

Unit Cell:

Length (Å) Angle (°)
a = 63.62 α = 109.38
b = 68.48 β = 92.66
c = 87.07 γ = 117.66

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2015-02-23
  • Released Date: 2015-03-04
  • Deposition author(s): Zhang, W., Collinet, B., Perrochia, L., Durand, D., Van Tilbeurgh, H.
  • Previous versions: 4WOS

Revision History

No revisions since initial release