8OYZ | pdb_00008oyz

Structure of the Histidine Kinase CheA ATP-Binding domain in complex with compound ODDHK10

PDB DOI: https://doi.org/10.2210/pdb8OYZ/pdb

Classification: SIGNALING PROTEIN
Organism(s): Thermotoga maritima
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-05-05 Released: 2024-05-15
Deposition Author(s): Adhav, A., Marina, A.
Funding Organization(s): H2020 Marie Curie Actions of the European Commission

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.242 (Depositor), 0.241 (DCC)
R-Value Work:
0.190 (Depositor), 0.190 (DCC)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Structure of the Histidine Kinase CheA ATP-Binding domain in complex with compound ODDHK10

Adhav, A., Marina, A.

To be published.

Macromolecule Content

Total Structure Weight: 42.48 kDa
Atom Count: 2,872
Modeled Residue Count: 344
Deposited Residue Count: 378
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chemotaxis protein CheA	A [auth B], B [auth A]	189	Thermotoga maritima	Mutation(s): 0 Gene Names: cheA, TM_0702 EC: 2.7.13.3
UniProt
Find proteins for Q56310 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q56310 Go to UniProtKB: Q56310
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q56310
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
WXC (Subject of Investigation/LOI) Query on WXC Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth B]	C [auth B], D [auth A]	2-azanyl-7,8-dihydro-6~{H}-quinazolin-5-one C₈ H₉ N₃ O ZXWJMLMXKMSYTP-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Focus chain D [auth A] Interactions & Density Focus chain C [auth B] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.242 (Depositor), 0.241 (DCC)
R-Value Work: 0.190 (Depositor), 0.190 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.958	α = 90
b = 59.133	β = 97.041
c = 66.837	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-05-15

Deposition Author(s):

Funding Organization	Location	Grant Number
H2020 Marie Curie Actions of the European Commission	European Union	765147

Revision History (Full details and data files)

Version 1.0: 2024-05-15
Type: Initial release

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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.