5MT6

Structure of E.coli GlpG in complex with peptide derived inhibitor Ac-RVRHA-phenylethyl-ketoamide

• PDB DOI: https://doi.org/10.2210/pdb5MT6/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli K-12, Providencia stuartii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2017-01-06 Released: 2017-11-15 
• Deposition Author(s): Vinothkumar, K.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.16 Å
• R-Value Free: 0.266 
• R-Value Work: 0.214 
• R-Value Observed: 0.216 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 21.77 kDa 
• Atom Count: 1,528 
• Modelled Residue Count: 187 
• Deposited Residue Count: 187 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rhomboid protease GlpG	A	180	Escherichia coli K-12	Mutation(s): 0  Gene Names: glpG, b3424, JW5687 EC: 3.4.21.105 Membrane Entity: Yes
UniProt
Find proteins for P09391 (Escherichia coli (strain K12)) Explore P09391  Go to UniProtKB:  P09391

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ACE-ARG-VAL-ARG-HIS-ALA-V9C	B	7	Providencia stuartii	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BNG	C [auth A], D [auth A]	nonyl beta-D-glucopyranoside C15 H30 O6 QFAPUKLCALRPLH-UXXRCYHCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.16 Å
• R-Value Free: 0.266 
• R-Value Work: 0.214 
• R-Value Observed: 0.216 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.71	α = 90
b = 111.71	β = 90
c = 124.229	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PHASER	phasing
XDS	data reduction
XDS	data scaling
Aimless	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-11-15 
Deposition Author(s): Vinothkumar, K.R.

Revision History  

• Version 1.0: 2017-11-15
  Type: Initial release
  
• Version 1.1: 2018-01-03
  Changes: Database references
• Version 1.2: 2019-05-08
  Changes: Advisory, Data collection, Derived calculations
• Version 1.3: 2019-07-10
  Changes: Data collection
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.5: 2024-01-17
  Changes: Data collection, Database references, Refinement description, Structure summary