3KI2 | pdb_00003ki2

Catalytic fragment of Cholix toxin from Vibrio Cholerae in complex with inhibitor GP-G

PDB DOI: https://doi.org/10.2210/pdb3KI2/pdb

Classification: Transferase,toxin
Organism(s): Vibrio cholerae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-10-31 Released: 2010-10-27
Deposition Author(s): Jorgensen, R., Edwards, P.R., Merrill, A.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.28 Å
R-Value Free:
0.205 (Depositor), 0.201 (DCC)
R-Value Work:
0.181 (Depositor), 0.178 (DCC)
R-Value Observed:
0.182 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structure function analysis of soluble inhibitors of cholix toxin from Vibrio cholerae

Jorgensen, R., Edwards, P.R., Merrill, A.R.

To be published.

Macromolecule Content

Total Structure Weight: 23.92 kDa
Atom Count: 1,903
Modeled Residue Count: 198
Deposited Residue Count: 211
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cholix toxin	A	211	Vibrio cholerae	Mutation(s): 0 Gene Names: chxa, toxA EC: 2.4.2.36
UniProt
Find proteins for Q5EK40 (Vibrio cholerae) Explore Q5EK40 Go to UniProtKB: Q5EK40
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5EK40
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
G9G Query on G9G Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	2-(4-methylpiperazin-1-yl)benzo[c][1,5]naphthyridin-6(5H)-one C₁₇ H₁₈ N₄ O YRVTWLAUEOBDFG-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.28 Å
R-Value Free: 0.205 (Depositor), 0.201 (DCC)
R-Value Work: 0.181 (Depositor), 0.178 (DCC)
R-Value Observed: 0.182 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.16	α = 90
b = 64.87	β = 90
c = 78.41	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
Macromolecular	data collection
XDS	data reduction
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2010-10-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-10-27
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.