6ARI | pdb_00006ari

Crystal structure of a dephospho-CoA kinase from Escherichia coli in complex with inhibitor CM078

PDB DOI: https://doi.org/10.2210/pdb6ARI/pdb

Classification: Transferase/Transferase Inhibitor
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-08-22 Released: 2018-08-22
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.208 (Depositor), 0.210 (DCC)
R-Value Work:
0.167 (Depositor), 0.170 (DCC)
R-Value Observed:
0.169 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of a dephospho-CoA kinase from Escherichia coli in complex with inhibitor CM078

Mayclin, S.J., Dranow, D.M., Lorimer, D., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 48.78 kDa
Atom Count: 3,465
Modeled Residue Count: 403
Deposited Residue Count: 428
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dephospho-CoA kinase	A, B	214	Escherichia coli K-12	Mutation(s): 0 Gene Names: coaE, yacE, b0103, JW0100 EC: 2.7.1.24
UniProt
Find proteins for P0A6I9 (Escherichia coli (strain K12)) Explore P0A6I9 Go to UniProtKB: P0A6I9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A6I9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BQV (Subject of Investigation/LOI) Query on BQV Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain D [auth A] MOL2 format, chain J [auth B] MOL2 format, chain D [auth A] mmCIF format, chain J [auth B] mmCIF format, chain D [auth A]	D [auth A], J [auth B]	N-(methylsulfonyl)-3-{[(thiophen-2-yl)sulfanyl]methyl}benzamide C₁₃ H₁₃ N O₃ S₃ VUNXNZBHBBHTIB-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain J [auth B]
CIT Query on CIT Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain C [auth A] MOL2 format, chain I [auth B] MOL2 format, chain C [auth A] mmCIF format, chain I [auth B] mmCIF format, chain C [auth A]	C [auth A], I [auth B]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain I [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] K [auth B] E [auth A], F [auth A], G [auth A], H [auth A], K [auth B], L [auth B], M [auth B], N [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B]