3ZMH

Structure of E.coli rhomboid protease GlpG in complex with monobactam L62

Structural Biology Knowledgebase: 3ZMH SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.229
  • R-Value Work: 0.188

Literature

Macromolecules
Sequence Display for 3ZMH

Classification: HYDROLASE

Total Structure Weight: 22773.19

Macromolecule Entities
Molecule Chains Length Organism Details
RHOMBOID PROTEASE GLPG A 180 Escherichia coli EC#: 3.4.21.105 IUBMB
Fragment: CORE TM DOMAIN, RESIDUES 91-270
Details: THE BETA LACTAM RING IS OPENED BY THE NUCLEOPHILIC ATTACK OF S201 ON C2-O1 TO FORM A COVALENT BOND
Gene Name(s): glpG b3424 JW5687
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Membrane Protein

Source: inferred by homology | Group: ALPHA-HELICAL

Subgroup Name: Intramembrane Proteases

Protein Name: GlpG rhomboid-family intramembrane protease


Small Molecules
Ligands 4 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 NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
L62
Query on L62

A cyclopentyl N-[(1R)-3-oxidanylidene-1-phenyl- propyl]carbamate
C15 H19 N O3
JHRUSYOIALPZLD-CQSZACIVSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
78C
Query on 78C

A CYCLOPENTYL 2-OXO-4-PHENYLAZETIDINE-1-CARBOXYLATE
C15 H17 N O3
HXGULOODWVYRBT-ZDUSSCGKSA-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)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
L62 N/A in BindingDB
N/A in BindingMoad
IC50: 5267 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.229
  • R-Value Work: 0.188
  • Space Group: H 3 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 110.15 α = 90.00
b = 110.15 β = 90.00
c = 128.63 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-02-11
  • Released Date: 2013-05-22
  • Deposition author(s): Vinothkumar, K.R., Pierrat, O.A., Large, J.M., Freeman, M.

Revision History

  • 2013-08-28
    Type: Citation | Details: JRNL
  • 2013-05-29
    Type: Citation | Details: JRNL