7JLL

The internal aldimine crystal structure of Salmonella typhimurium Tryptophan Synthase mutant beta-S377A in complex with inhibitor 2-({[4-(trifluoromethoxy)phenyl]sulfonyl}amino)ethyl dihydrogen phosphate (F9F) at the alpha-site, Cesium ion at the metal coordination site and L-Tryptophan at the enzyme beta-site

PDB DOI: https://doi.org/10.2210/pdb7JLL/pdb

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

Deposited: 2020-07-29 Released: 2021-08-04
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: 1.55 Å
R-Value Free: 0.215
R-Value Work: 0.185
R-Value Observed: 0.186

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 internal aldimine crystal structure of Salmonella typhimurium Tryptophan Synthase mutant beta-S377A in complex with inhibitor 2-({[4-(trifluoromethoxy)phenyl]sulfonyl}amino)ethyl dihydrogen phosphate (F9F) at the alpha-site, Cesium ion at the metal coordination site and L-Tryptophan at the enzyme beta-site.

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

To be published.

Macromolecule Content

Total Structure Weight: 76 kDa
Atom Count: 6,094
Modelled Residue Count: 662
Deposited Residue Count: 665
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00929
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A2K1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 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 I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	2-({[4-(TRIFLUOROMETHOXY)PHENYL]SULFONYL}AMINO)ETHYL DIHYDROGEN PHOSPHATE C₉ H₁₁ F₃ N O₇ P S JDDKDMFCTOZVCJ-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
PLP (Subject of Investigation/LOI) Query on PLP Download Ideal Coordinates CCD File SDF format, chain JA [auth B] MOL2 format, chain JA [auth B] mmCIF format, chain JA [auth B]	JA [auth B]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain JA [auth B] Interactions & Density Focus chain JA [auth B]
TRP (Subject of Investigation/LOI) Query on TRP Download Ideal Coordinates CCD File SDF format, chain IA [auth B] SDF format, chain K [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain K [auth A] mmCIF format, chain IA [auth B] mmCIF format, chain K [auth A]	IA [auth B], K [auth A]	TRYPTOPHAN C₁₁ H₁₂ N₂ O₂ QIVBCDIJIAJPQS-VIFPVBQESA-N		Interactions Focus chain IA [auth B] Focus chain K [auth A] Interactions & Density Focus chain IA [auth B] Focus chain K [auth A]
CS (Subject of Investigation/LOI) Query on CS Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain TA [auth B] SDF format, chain UA [auth B] MOL2 format, chain J [auth A] MOL2 format, chain TA [auth B] MOL2 format, chain UA [auth B] mmCIF format, chain J [auth A] mmCIF format, chain TA [auth B] mmCIF format, chain UA [auth B]	J [auth A], TA [auth B], UA [auth B]	CESIUM ION Cs NCMHKCKGHRPLCM-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain TA [auth B] Focus chain UA [auth B] Interactions & Density Focus chain J [auth A] Focus chain TA [auth B] Focus chain UA [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain P [auth A] MOL2 format, chain P [auth A] mmCIF format, chain P [auth A]	P [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain P [auth A] Interactions & Density Focus chain P [auth A]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth A] SDF format, chain EA [auth B] SDF format, chain H [auth A] SDF format, chain M [auth A] SDF format, chain MA [auth B] SDF format, chain NA [auth B] SDF format, chain OA [auth B] SDF format, chain PA [auth B] SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain D [auth A] SDF format, chain DA [auth B] SDF format, chain F [auth A] SDF format, chain FA [auth B] SDF format, chain G [auth A] SDF format, chain GA [auth B] SDF format, chain HA [auth B] SDF format, chain KA [auth B] SDF format, chain L [auth A] SDF format, chain LA [auth B] SDF format, chain N [auth A] SDF format, chain O [auth A] MOL2 format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain H [auth A] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth B] MOL2 format, chain NA [auth B] MOL2 format, chain OA [auth B] MOL2 format, chain PA [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain D [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain KA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] mmCIF format, chain C [auth A] mmCIF format, chain E [auth A] mmCIF format, chain EA [auth B] mmCIF format, chain H [auth A] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth B] mmCIF format, chain NA [auth B] mmCIF format, chain OA [auth B] mmCIF format, chain PA [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain D [auth A] mmCIF format, chain DA [auth B] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth B] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain HA [auth B] mmCIF format, chain KA [auth B] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth B] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A]	AA [auth B] BA [auth B] C [auth A] CA [auth B] D [auth A] AA [auth B], BA [auth B], C [auth A], CA [auth B], D [auth A], DA [auth B], E [auth A], EA [auth B], F [auth A], FA [auth B], G [auth A], GA [auth B], H [auth A], HA [auth B], KA [auth B], L [auth A], LA [auth B], M [auth A], MA [auth B], N [auth A], NA [auth B], O [auth A], OA [auth B], PA [auth B]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain C [auth A] Focus chain CA [auth B] Focus chain D [auth A] Focus chain DA [auth B] Focus chain E [auth A] Focus chain EA [auth B] Focus chain F [auth A] Focus chain FA [auth B] Focus chain G [auth A] Focus chain GA [auth B] Focus chain H [auth A] Focus chain HA [auth B] Focus chain KA [auth B] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A] Focus chain OA [auth B] Focus chain PA [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain C [auth A] Focus chain CA [auth B] Focus chain D [auth A] Focus chain DA [auth B] Focus chain E [auth A] Focus chain EA [auth B] Focus chain F [auth A] Focus chain FA [auth B] Focus chain G [auth A] Focus chain GA [auth B] Focus chain H [auth A] Focus chain HA [auth B] Focus chain KA [auth B] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A] Focus chain OA [auth B] Focus chain PA [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain RA [auth B] SDF format, chain SA [auth B] SDF format, chain QA [auth B] MOL2 format, chain RA [auth B] MOL2 format, chain SA [auth B] MOL2 format, chain QA [auth B] mmCIF format, chain RA [auth B] mmCIF format, chain SA [auth B] mmCIF format, chain QA [auth B]	QA [auth B], RA [auth B], SA [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain QA [auth B] Focus chain RA [auth B] Focus chain SA [auth B] Interactions & Density Focus chain QA [auth B] Focus chain RA [auth B] Focus chain SA [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AB [auth B] SDF format, chain BB [auth B] SDF format, chain CB [auth B] SDF format, chain DB [auth B] SDF format, chain GB [auth B] SDF format, chain HB [auth B] SDF format, chain R [auth A] SDF format, chain T [auth A] SDF format, chain V [auth A] SDF format, chain W [auth A] SDF format, chain WA [auth B] SDF format, chain X [auth A] SDF format, chain YA [auth B] SDF format, chain ZA [auth B] SDF format, chain EB [auth B] SDF format, chain FB [auth B] SDF format, chain Q [auth A] SDF format, chain S [auth A] SDF format, chain U [auth A] SDF format, chain VA [auth B] SDF format, chain XA [auth B] SDF format, chain Y [auth A] SDF format, chain Z [auth A] MOL2 format, chain AB [auth B] MOL2 format, chain BB [auth B] MOL2 format, chain CB [auth B] MOL2 format, chain DB [auth B] MOL2 format, chain GB [auth B] MOL2 format, chain HB [auth B] MOL2 format, chain R [auth A] MOL2 format, chain T [auth A] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] MOL2 format, chain WA [auth B] MOL2 format, chain X [auth A] MOL2 format, chain YA [auth B] MOL2 format, chain ZA [auth B] MOL2 format, chain EB [auth B] MOL2 format, chain FB [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain S [auth A] MOL2 format, chain U [auth A] MOL2 format, chain VA [auth B] MOL2 format, chain XA [auth B] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A] mmCIF format, chain AB [auth B] mmCIF format, chain BB [auth B] mmCIF format, chain CB [auth B] mmCIF format, chain DB [auth B] mmCIF format, chain GB [auth B] mmCIF format, chain HB [auth B] mmCIF format, chain R [auth A] mmCIF format, chain T [auth A] mmCIF format, chain V [auth A] mmCIF format, chain W [auth A] mmCIF format, chain WA [auth B] mmCIF format, chain X [auth A] mmCIF format, chain YA [auth B] mmCIF format, chain ZA [auth B] mmCIF format, chain EB [auth B] mmCIF format, chain FB [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain S [auth A] mmCIF format, chain U [auth A] mmCIF format, chain VA [auth B] mmCIF format, chain XA [auth B] mmCIF format, chain Y [auth A] mmCIF format, chain Z [auth A]	AB [auth B] BB [auth B] CB [auth B] DB [auth B] EB [auth B] AB [auth B], BB [auth B], CB [auth B], DB [auth B], EB [auth B], FB [auth B], GB [auth B], HB [auth B], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], VA [auth B], W [auth A], WA [auth B], X [auth A], XA [auth B], Y [auth A], YA [auth B], Z [auth A], ZA [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AB [auth B] Focus chain BB [auth B] Focus chain CB [auth B] Focus chain DB [auth B] Focus chain EB [auth B] Focus chain FB [auth B] Focus chain GB [auth B] Focus chain HB [auth B] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain VA [auth B] Focus chain W [auth A] Focus chain WA [auth B] Focus chain X [auth A] Focus chain XA [auth B] Focus chain Y [auth A] Focus chain YA [auth B] Focus chain Z [auth A] Focus chain ZA [auth B] Interactions & Density Focus chain AB [auth B] Focus chain BB [auth B] Focus chain CB [auth B] Focus chain DB [auth B] Focus chain EB [auth B] Focus chain FB [auth B] Focus chain GB [auth B] Focus chain HB [auth B] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain VA [auth B] Focus chain W [auth A] Focus chain WA [auth B] Focus chain X [auth A] Focus chain XA [auth B] Focus chain Y [auth A] Focus chain YA [auth B] Focus chain Z [auth A] Focus chain ZA [auth B]