2GJ8

Structure of the MnmE G-domain in complex with GDP*AlF4-, Mg2+ and K+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.256
  • R-Value Work: 0.205

Literature

Macromolecules
Sequence Display for 2GJ8

Classification: HYDROLASE

Total Structure Weight: 78281.15

Macromolecule Entities
Molecule Chains Length Organism Details
tRNA modification GTPase trmE A, B, C, D 172 Escherichia coli EC#: 3.6 IUBMB
Fragment: G-domain (216-384)
Mutation: M217M, M264M, M302M, M346M, M376M, M382M
Gene Name(s): mnmE thdF trmE b3706 JW3684
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
GDP
Query on GDP

A, B, C, D GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ALF
Query on ALF

A, B, C, D TETRAFLUOROALUMINATE ION
Al F4
UYOMQIYKOOHAMK-UHFFFAOYSA-J
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SE
Query on SE

A, C, D SELENIUM ATOM
Se
SPVXKVOXSXTJOY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
K
Query on K

A, B, C, D POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B, C, D MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-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, B, C, D L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.256
  • R-Value Work: 0.205
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 57.54 α = 90.00
b = 70.23 β = 95.51
c = 91.30 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-03-30
  • Released Date: 2006-07-04
  • Deposition author(s): Scrima, A., Wittinghofer, A.

Revision History

  • 2008-05-01
    Type: Version format compliance
  • 2011-07-13
    Type: Version format compliance