1KJI

Crystal structure of glycinamide ribonucleotide transformylase in complex with Mg-AMPPCP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.229
  • R-Value Work: 0.183

Literature

Macromolecules
Sequence Display for 1KJI

Classification: TRANSFERASE

Total Structure Weight: 86182.07

Macromolecule Entities
Molecule Chains Length Organism Details
phosphoribosylglycinamide formyltransferase 2 A, B 391 Escherichia coli EC#: 2.1.2 IUBMB
Gene Name(s): purT b1849 JW1838
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE (Synonym)
C11 H18 N5 O12 P3
UFZTZBNSLXELAL-IOSLPCCCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MPO
Query on MPO

A 3[N-MORPHOLINO]PROPANE SULFONIC ACID
C7 H15 N O4 S
DVLFYONBTKHTER-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)
CL
Query on CL

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
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)
NA
Query on NA

A, B SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.229
  • R-Value Work: 0.183
  • Space Group: P 21 21 2

Unit Cell:

Length (Å) Angle (°)
a = 62.20 α = 90.00
b = 179.20 β = 90.00
c = 76.20 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-12-04
  • Released Date: 2002-06-28
  • Deposition author(s): Thoden, J.B., Firestine, S.M., Benkovic, S.J., Holden, H.M.

Revision History

  • Version 1_0: 2002-06-28

    Type: Initial release

  • Version 1_1: 2008-04-27

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Version format compliance

  • Version 1_3: 2017-10-11

    Type: Refinement description