8AB5

Structure of E. coli GlpG in complex with peptide derived inhibitor Ac-VRHA-conh-[4-(4-butyl)-phenoxy-1-phenyl-2-butyl]

PDB DOI: https://doi.org/10.2210/pdb8AB5/pdb

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

Deposited: 2022-07-04 Released: 2023-10-25
Deposition Author(s): Skerlova, J., Polovinkin, V., Bach, K., Borshchevskiy, V., Strisovsky, K.
Funding Organization(s): Ministry of Science and Higher Education of the Russian Federation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.271
R-Value Work: 0.217
R-Value Observed: 0.220

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structure of E. coli GlpG in complex with peptide derived inhibitor Ac-VRHA-conh-[4-(4-butyl)-phenoxy-1-phenyl-2-butyl]

Skerlova, J., Polovinkin, V., Borshchevskiy, V., Strisovsky, K.

To be published.

Macromolecule Content

Total Structure Weight: 42.32 kDa
Atom Count: 2,980
Modelled Residue Count: 366
Deposited Residue Count: 370
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rhomboid protease GlpG	A, B	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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P09391
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ac-VRHA-conh-[4-(4-butyl)-phenoxy-1-phenyl-2-butyl]	C, D	5	Providencia stuartii	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002417 Query on PRD_002417	C, D	Ac-VRHA-conh-[4-(4-butyl)-phenoxy-1-phenyl-2-butyl]	Peptide-like / Inhibitor		Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.271
R-Value Work: 0.217
R-Value Observed: 0.220
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.54	α = 90
b = 70.86	β = 100.06
c = 66	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-10-25

Deposition Author(s):

Borshchevskiy, V.

Funding Organization	Location	Grant Number
Ministry of Science and Higher Education of the Russian Federation	Russian Federation	075-15-2021-1354

Revision History (Full details and data files)

Version 1.0: 2023-10-25
Type: Initial release

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.