3ZEB

A complex of GlpG with isocoumarin inhibitor covalently bonded to serine 201 and histidine 150

Structural Biology Knowledgebase: 3ZEB SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.247
  • R-Value Work: 0.214

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3ZEB

Classification: HYDROLASE

Total Structure Weight: 22064.92

Macromolecule Entities
Molecule Chains Length Organism Details
RHOMBOID PROTEASE GLPG A 179 Escherichia coli EC#: 3.4.21.105 IUBMB
Fragment: CORE TM DOMAIN, RESIDUES 92-270
Details: THE ISOCOUMARIN RING IS OPENED BY THE NUCLEOPHILIC ATTACK OF S201 FORMS ESTER BOND AND SUBSEQUENTLY A REACTION BETWEEN HISTIDINE CREATES A SECOND COVALENT BOND.
Gene Name(s): glpG b3424 JW5687

Membrane Protein

Source: inferred by homology | Group: ALPHA-HELICAL

Subgroup Name: Intramembrane Proteases

Protein Name: GlpG rhomboid-family intramembrane protease


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

A B-NONYLGLUCOSIDE
C15 H30 O6
QFAPUKLCALRPLH-UXXRCYHCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SV1
Query on SV1

A 2-phenylethyl 2-(4-azanyl-2-methanoyl-phenyl)ethanoate
C17 H17 N O3
VKURJRUODVXQJZ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.247
  • R-Value Work: 0.214
  • Space Group: H 3 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 111.11 α = 90.00
b = 111.11 β = 90.00
c = 126.07 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-12-04
  • Released Date: 2013-02-13
  • Deposition author(s): Vinothkumar, K.R., voskya, O., Kuettler, E.V., Brouwer, A.J., Liskamp, R.M.J., Verhelst, S.H.L.

Revision History

  • 2013-03-06
    Type: Citation | Details: JRNL