8VL8 | pdb_00008vl8

Salmonella enterica Typhimurium taxis to serine and repellents (Tsr) ligand-binding domain with L-Ser, pH 7

PDB DOI: https://doi.org/10.2210/pdb8VL8/pdb

Classification: SIGNALING PROTEIN
Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
Expression System: Escherichia coli K-12
Mutation(s): No

Deposited: 2024-01-11 Released: 2024-04-03
Deposition Author(s): Glenn, S., Baylink, A.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.273 (Depositor), 0.271 (DCC)
R-Value Work:
0.226 (Depositor), 0.225 (DCC)
R-Value Observed:
0.228 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Human Serum is a Potent Chemoattractant for Enterobacteriaceae Species Associated with Gastrointestinal Bleeding

Glenn, S., Gentry-Lear, Z., Shavlik, M., Harms, M.J., Asaki, T.J., Baylink, A.

(2024) Elife

DOI: https://doi.org/10.7554/eLife.93178.1

Macromolecule Content

Total Structure Weight: 95.7 kDa
Atom Count: 5,839
Modeled Residue Count: 698
Deposited Residue Count: 815
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methyl-accepting chemotaxis protein	A, B, C, D, E	163	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0 Gene Names: G0L35_02695
UniProt
Find proteins for Q8ZJY4 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q8ZJY4 Go to UniProtKB: Q8ZJY4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8ZJY4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SER (Subject of Investigation/LOI) Query on SER Download:Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain R [auth B] SDF format, chain V [auth C] SDF format, chain Z [auth D] SDF format, chain G [auth A] MOL2 format, chain BA [auth E] MOL2 format, chain R [auth B] MOL2 format, chain V [auth C] MOL2 format, chain Z [auth D] MOL2 format, chain G [auth A] mmCIF format, chain BA [auth E] mmCIF format, chain R [auth B] mmCIF format, chain V [auth C] mmCIF format, chain Z [auth D] mmCIF format, chain G [auth A]	BA [auth E], G [auth A], R [auth B], V [auth C], Z [auth D]	SERINE C₃ H₇ N O₃ MTCFGRXMJLQNBG-REOHCLBHSA-N		Interactions Focus chain BA [auth E] Focus chain G [auth A] Focus chain R [auth B] Focus chain V [auth C] Focus chain Z [auth D] Interactions & Density Focus chain BA [auth E] Focus chain G [auth A] Focus chain R [auth B] Focus chain V [auth C] Focus chain Z [auth D]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain Q [auth B] SDF format, chain X [auth D] SDF format, chain Y [auth D] SDF format, chain U [auth C] SDF format, chain P [auth B] SDF format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain U [auth C] MOL2 format, chain P [auth B] MOL2 format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain X [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain U [auth C] mmCIF format, chain P [auth B] mmCIF format, chain H [auth A]	H [auth A] I [auth A] P [auth B] Q [auth B] U [auth C] H [auth A], I [auth A], P [auth B], Q [auth B], U [auth C], X [auth D], Y [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain U [auth C] Focus chain X [auth D] Focus chain Y [auth D] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain U [auth C] Focus chain X [auth D] Focus chain Y [auth D]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain S [auth C] SDF format, chain W [auth D] SDF format, chain T [auth C] MOL2 format, chain AA [auth E] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain S [auth C] MOL2 format, chain W [auth D] MOL2 format, chain T [auth C] mmCIF format, chain AA [auth E] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain S [auth C] mmCIF format, chain W [auth D] mmCIF format, chain T [auth C]	AA [auth E] F [auth A] K [auth B] L [auth B] M [auth B] AA [auth E], F [auth A], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], S [auth C], T [auth C], W [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain F [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain W [auth D] Interactions & Density Focus chain AA [auth E] Focus chain F [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain W [auth D]