3ZOT

Structure of E.coli rhomboid protease GlpG in complex with monobactam L29 (data set 2)

PDB DOI: https://doi.org/10.2210/pdb3ZOT/pdb

Classification: HYDROLASE
Organism(s): Escherichia coli BL21(DE3)
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No
Membrane Protein: Yes PDBTMMemProtMD

Deposited: 2013-02-24 Released: 2013-05-22
Deposition Author(s): Vinothkumar, K.R., Pierrat, O.A., Large, J.M., Freeman, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.252
R-Value Work: 0.198
R-Value Observed: 0.201

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 23.43 kDa
Atom Count: 1,540
Modelled Residue Count: 178
Deposited Residue Count: 180
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RHOMBOID PROTEASE GLPG	A	180	Escherichia coli BL21(DE3)	Mutation(s): 0 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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BNG Query on BNG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A]	nonyl beta-D-glucopyranoside C₁₅ H₃₀ O₆ QFAPUKLCALRPLH-UXXRCYHCSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A]
L6C Query on L6C Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	phenyl N-[(1R)-3-oxidanylidene-1-phenyl-propyl]carbamate C₁₆ H₁₅ N O₃ HHWCOMIRIZKFCW-OAHLLOKOSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A]	L [auth A], M [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain L [auth A] Focus chain M [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
L6C	PDBBind: 3ZOT	IC50: 1117 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.252
R-Value Work: 0.198
R-Value Observed: 0.201
Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.2	α = 90
b = 110.2	β = 90
c = 128.9	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-05-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-05-22
Type: Initial release
Version 1.1: 2013-05-29
Changes: Database references
Version 1.2: 2013-08-28
Changes: Database references
Version 1.3: 2019-02-27
Changes: Data collection, Derived calculations, Experimental preparation, Other
Version 1.4: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Other, Structure summary
Version 1.5: 2023-12-20
Changes: Data collection, Database references, Refinement description, Structure summary

Prepare Data

Validate Data

Deposit Data

Help and Resources

3ZOT

Structure of E.coli rhomboid protease GlpG in complex with monobactam L29 (data set 2)

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)