7JTT | pdb_00007jtt

The external aldimine crystal structure of Salmonella typhimurium Tryptophan Synthase mutant beta-S377A in complex F9 inhibitor at the alpha-site and cesium ion at the metal coordination site. The single beta-Q114 rotamer conformation allows a hydrogen bond to form with the PLP oxygen at the position 3 in the ring

PDB DOI: https://doi.org/10.2210/pdb7JTT/pdb

Classification: LYASE/LYASE INHIBITOR
Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2020-08-18 Released: 2021-08-25
Deposition Author(s): Hilario, E., Dunn, M.F., Mueller, L.J.
Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.64 Å
R-Value Free:
0.218 (Depositor), 0.219 (DCC)
R-Value Work:
0.188 (Depositor), 0.188 (DCC)
R-Value Observed:
0.189 (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

The external aldimine crystal structure of Salmonella typhimurium Tryptophan Synthase mutant beta-S377A in complex F9 inhibitor at the alpha-site and cesium ion at the metal coordination site. The single beta-Q114 rotamer conformation allows a hydrogen bond to form with the PLP oxygen at the position 3 in the ring.

Hilario, E., Dunn, M.F., Mueller, L.J.

To be published.

Macromolecule Content

Total Structure Weight: 75.12 kDa
Atom Count: 5,946
Modeled Residue Count: 664
Deposited Residue Count: 665
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tryptophan synthase alpha chain	A	268	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 0 Gene Names: trpA, STM1727 EC: 4.2.1.20
UniProt
Find proteins for P00929 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P00929 Go to UniProtKB: P00929
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00929
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tryptophan synthase beta chain	B	397	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 1 Gene Names: trpB, STM1726 EC: 4.2.1.20
UniProt
Find proteins for P0A2K1 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P0A2K1 Go to UniProtKB: P0A2K1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A2K1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
F9F (Subject of Investigation/LOI) Query on F9F Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	2-({[4-(TRIFLUOROMETHOXY)PHENYL]SULFONYL}AMINO)ETHYL DIHYDROGEN PHOSPHATE C₉ H₁₁ F₃ N O₇ P S JDDKDMFCTOZVCJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
KOU (Subject of Investigation/LOI) Query on KOU Download:Ideal Coordinates CCD File SDF format, chain CA [auth B] MOL2 format, chain CA [auth B] mmCIF format, chain CA [auth B]	CA [auth B]	(E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-serine C₁₁ H₁₅ N₂ O₈ P ZTQZHYMXYBDMIL-BIMOUXMDSA-N		Interactions Focus chain CA [auth B] Interactions & Density Focus chain CA [auth B]
CS (Subject of Investigation/LOI) Query on CS Download:Ideal Coordinates CCD File SDF format, chain MA [auth B] SDF format, chain NA [auth B] MOL2 format, chain MA [auth B] MOL2 format, chain NA [auth B] mmCIF format, chain MA [auth B] mmCIF format, chain NA [auth B]	MA [auth B], NA [auth B]	CESIUM ION Cs NCMHKCKGHRPLCM-UHFFFAOYSA-N		Interactions Focus chain MA [auth B] Focus chain NA [auth B] Interactions & Density Focus chain MA [auth B] Focus chain NA [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain DA [auth B] MOL2 format, chain DA [auth B] mmCIF format, chain DA [auth B]	DA [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain DA [auth B] Interactions & Density Focus chain DA [auth B]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain E [auth A] SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain LA [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain Q [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain R [auth B] SDF format, chain P [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain D [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain LA [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain R [auth B] MOL2 format, chain P [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain D [auth A] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain E [auth A] mmCIF format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain LA [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain R [auth B] mmCIF format, chain P [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain D [auth A]	AA [auth B] BA [auth B] D [auth A] E [auth A] F [auth A] AA [auth B], BA [auth B], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], K [auth B], L [auth B], LA [auth B], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] 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 K [auth B] Focus chain L [auth B] Focus chain LA [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] 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 K [auth B] Focus chain L [auth B] Focus chain LA [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain EA [auth B] SDF format, chain FA [auth B] SDF format, chain GA [auth B] SDF format, chain IA [auth B] SDF format, chain KA [auth B] SDF format, chain JA [auth B] SDF format, chain HA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain KA [auth B] MOL2 format, chain JA [auth B] MOL2 format, chain HA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain IA [auth B] mmCIF format, chain KA [auth B] mmCIF format, chain JA [auth B] mmCIF format, chain HA [auth B]	EA [auth B] FA [auth B] GA [auth B] HA [auth B] IA [auth B] EA [auth B], FA [auth B], GA [auth B], HA [auth B], IA [auth B], JA [auth B], KA [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain KA [auth B] Interactions & Density Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain KA [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain PA [auth B] SDF format, chain OA [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain PA [auth B] MOL2 format, chain OA [auth B] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain PA [auth B] mmCIF format, chain OA [auth B]	I [auth A], J [auth A], OA [auth B], PA [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain OA [auth B] Focus chain PA [auth B] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain OA [auth B] Focus chain PA [auth B]