2DG5

Crystal Structure of Gamma-glutamyl transpeptidase from Escherichia coli in complex with hydrolyzed Glutathione

Structural Biology Knowledgebase: 2DG5 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.195
  • R-Value Work: 0.179

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2DG5

Classification: Transferase

Total Structure Weight: 120647.74

Macromolecule Entities
Molecule Chains Length Organism Details
Gamma-glutamyltranspeptidase A, C 366 Escherichia coli EC#: 2.3.2.2 IUBMB
Fragment: LARGE SUBUNIT
Mutation: M50M, M99M, M116M, M125M, M164M, M233M, M255M, M290M, M312M, M323M, M326M
Gene Name(s): ggt b3447 JW3412
Gamma-glutamyltranspeptidase B, D 190 Escherichia coli EC#: 2.3.2.2 IUBMB
Fragment: SMALL SUBUNIT
Mutation: M431M, M464M, M494M, M550M, M557M
Gene Name(s): ggt b3447 JW3412

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

B, D GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

B, D CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
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: 1.6 Å
  • R-Value Free: 0.195
  • R-Value Work: 0.179
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 78.14 α = 90.00
b = 126.60 β = 90.00
c = 129.20 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-03-08
  • Released Date: 2006-04-18
  • Deposition author(s): Okada, T., Wada, K., Fukuyama, K.

Revision History

  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4