6duc

Crystal structure of mutant beta-K167T tryptophan synthase in complex with inhibitor N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the alpha-site, cesium ion at the metal coordination site, and 2-aminophenol quinonoid (1D0) at the beta-site

Method: X-RAY DIFFRACTION D_max: 91.8 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Tryptophan synthase alpha chain

Salmonella typhimurium

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–268	Not recorded	Tryptophan synthase beta chain × 2 （A0A0J0ZFZ1） F9F 2-({[4-(TRIFLUOROMETHOXY)PHENYL]SULFONYL}AMINO)ETHYL DIHYDROGEN PHOSPHATE × 2 DMS DIMETHYL SULFOXIDE × 12 EDO 1,2-ETHANEDIOL × 6 CL CHLORIDE ION × 22 1D0 (2E)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)imino]-3-[(2-hydroxyphenyl)amino]propanoic acid × 2 2AP 2-AMINOPYRIDINE × 2 CS CESIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.9；297 K；50 mM Bicine-Cs, 10-12% PEG3350, 50 mM cesium chloride, 4-8 mM spermine	Resolution 1.79 Å R-free 0.232

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 6DUC	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6O1H Tryptophan synthase Q114A mutant in complex with N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the enzyme alpha-site, cesium ion at the metal coordination site, and 2-aminophenol quinonoid at the enzyme beta site Deposited 2019-02-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–268（268 aa）	Not recorded	DMS DIMETHYL SULFOXIDE × 16 F9F 2-({[4-(TRIFLUOROMETHOXY)PHENYL]SULFONYL}AMINO)ETHYL DIHYDROGEN PHOSPHATE × 2 CS CESIUM ION × 6 CL CHLORIDE ION × 32 HVK pyridin-2-amine × 2 1D0 (2E)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)imino]-3-[(2-hydroxyphenyl)amino]propanoic acid × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；293 K；100 mM Bicine-CsOH, pH 7.8, 5-10% PEG8000, 2 mM F9F, 0.01 mM PLP	Resolution 1.64 Å R-free 0.199
6VFD Tryptophan synthase mutant Q114A in complex with cesium ion at the metal coordination site and 2-aminophenol quinonoid at the enzyme beta site Deposited 2020-01-03	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–268（268 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 8 SER SERINE × 4 DMS DIMETHYL SULFOXIDE × 20 CL CHLORIDE ION × 32 1D0 (2E)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)imino]-3-[(2-hydroxyphenyl)amino]propanoic acid × 2 CS CESIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；293 K；50 mM Bicine-CsOH, 10% PEG 8,000, 4 mM spermine	Resolution 1.70 Å R-free 0.224
6WX3 High resolution Tryptophan Synthase crystal structure from Salmonella typhimurium in complex with F9 inhibitor in the alpha-site, Cesium ion at the metal coordination site and internal aldimine form. Deposited 2020-05-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–268（268 aa）	Not recorded	F9F 2-({[4-(TRIFLUOROMETHOXY)PHENYL]SULFONYL}AMINO)ETHYL DIHYDROGEN PHOSPHATE × 2 CL CHLORIDE ION × 2 PLP PYRIDOXAL-5'-PHOSPHATE × 2 CS CESIUM ION × 4 BCN BICINE × 8 EDO 1,2-ETHANEDIOL × 4 DMS DIMETHYL SULFOXIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；298 K；50 mM Bicine-CsOH, 10% PEG 8,000, 2 mM Spermine, pH 7.8	Resolution 1.20 Å R-free 0.181
6XIN The crystal structure of tryptophan synthase from Salmonella enterica serovar typhimurium in complex with (2S)-3-Amino-3-imino-2-phenyldiazenylpropanamide at the enzyme alpha-site. Deposited 2020-06-20	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–268（268 aa）	Not recorded	CL CHLORIDE ION × 28 DMS DIMETHYL SULFOXIDE × 48 EDO 1,2-ETHANEDIOL × 32 PGE TRIETHYLENE GLYCOL × 2 PEG DI(HYDROXYETHYL)ETHER × 2 PLP PYRIDOXAL-5'-PHOSPHATE × 2 V41 (2R,3Z)-3-amino-3-imino-2-[(E)-phenyldiazenyl]propanamide × 2 CS CESIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；298 K；50 mM Bicine-CsOH, 8% PEG 8,000, 2 mM Spermine, pH 7.8, 50mM (2S)-3-Amino-3-imino-2-phenyldiazenylpropanamide	Resolution 1.75 Å R-free 0.204
6XNC Salmonella typhimurium tryptophan synthase complexed with L-tryptophan and D-glycerol-3-phosphate Deposited 2020-07-02	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–268（268 aa）	Not recorded	DMS DIMETHYL SULFOXIDE × 56 1GP SN-GLYCEROL-1-PHOSPHATE × 2 NA SODIUM ION × 2 PLP PYRIDOXAL-5'-PHOSPHATE × 2 TRP TRYPTOPHAN × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.05 M Bicine-Na, pH 7.8, 1 mM EDTA, 1 mM DTT, 0.1 mM PLP, 1 mM spermine tetrahydrochloride, 10-12% PEG 3350, 6-10% glycerol	Resolution 2.11 Å R-free 0.213
6XOY Salmonella typhimurium tryptophan synthase complexed with D-tryptophan and D-glycerol-3-phosphate Deposited 2020-07-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–268（268 aa）	Not recorded	DMS DIMETHYL SULFOXIDE × 20 1GP SN-GLYCEROL-1-PHOSPHATE × 2 VB4 (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-D-tryptophan × 2 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；0.05 M Bicine-Na, pH 7.8, 5 mM Na2EDTA, 0.1 mM PLP, 1 mM DTT, 1 mM spermine tetrahydrochloride, 10-12% PEG 3350, 6-10% glycerol	Resolution 1.64 Å R-free 0.213
6XRH Salmonella typhimurium tryptophan synthase complexed with oxindolyl-L-alanine and D-glycerol-3-phosphate Deposited 2020-07-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–268（268 aa）	Not recorded	DMS DIMETHYL SULFOXIDE × 28 1GP SN-GLYCEROL-1-PHOSPHATE × 2 VCP (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-3-[(3S)-2-oxo-2,3-dihydro-1H-indol-3-yl]-L-alanine × 2 VCS 4-[(E)-({1-carboxy-2-[(3S)-2-oxo-2,3-dihydro-1H-indol-3-yl]ethan-1-id-1-yl}iminio)methyl]-2-methyl-5-[(phosphonooxy)methyl]pyridin-1-ium-3-olate × 2 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；0.05 M Bicine-Na, pH 7.8, 1 mM EDTA, 0.1 mM PLP, 1 mM DTT, and 1 mM spermine tetrahydrochloride, containing 10-12% PEG 3350 and 6-10% glycerol	Resolution 1.44 Å R-free 0.198
6XT0 Salmonella typhimurium tryptophan synthase complexed with dioxindolyl-L-alanine and D-glycerol-3-phosphate Deposited 2020-07-16	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–268（268 aa）	Not recorded	DMS DIMETHYL SULFOXIDE × 30 1GP SN-GLYCEROL-1-PHOSPHATE × 2 X9D 4-[(E)-({1-carboxy-2-[(3R)-3-hydroxy-2-oxo-2,3-dihydro-1H-indol-3-yl]ethan-1-id-1-yl}iminio)methyl]-2-methyl-5-[(phosphonooxy)methyl]pyridin-1-ium-3-olate × 2 VE4 4-[(E)-({1-carboxy-2-[(3R)-3-hydroxy-2-oxo-2,3-dihydro-1H-indol-3-yl]ethan-1-id-1-yl}iminio)methyl]-2-methyl-5-[(phosphonooxy)methyl]pyridin-1-ium-3-olate × 2 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；0.05 M bicine, pH 7.8, 5 mM EDTA, 0.1 mM PLP, 1 mM DTT, and 1 mM spermine tetrahydrochloride with 6-8% glycerol and 10-12% PEG 3350	Resolution 1.37 Å R-free 0.198
7A20 Azobenzene-Based Inhibitors for Tryptophan Synthase Deposited 2020-08-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–268（268 aa） Chain B 1–268（268 aa） Chain C 1–268（268 aa） Chain D 1–268（268 aa）	Not recorded	NA SODIUM ION × 2 144 TRIS-HYDROXYMETHYL-METHYL-AMMONIUM × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；291 K；PEG 8000, 0.1 M sodium citrate	Resolution 2.50 Å R-free 0.250
7KWV The aminoacrylate form of the wild-type Salmonella typhimurium Tryptophan Synthase in complex with inhibitor N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the enzyme alpha-site and cesium ion at the metal coordination site at 1.30 Angstrom resolution Deposited 2020-12-02	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–268（268 aa）	Not recorded	F9F 2-({[4-(TRIFLUOROMETHOXY)PHENYL]SULFONYL}AMINO)ETHYL DIHYDROGEN PHOSPHATE × 2 EDO 1,2-ETHANEDIOL × 10 CL CHLORIDE ION × 2 0JO 2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid × 2 PEG DI(HYDROXYETHYL)ETHER × 2 BCN BICINE × 6 CS CESIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；298 K；50 mM Bicine-CsOH, 10% PEG 8,000, 2 mM Spermine, pH 7.8	Resolution 1.30 Å R-free 0.199
7KXC The aminoacrylate form of the wild-type Salmonella typhimurium Tryptophan Synthase in complex with inhibitor N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the enzyme alpha-site, sodium ion at the metal coordination site and benzimidazole (BZI) at the enzyme beta-site at 1.30 Angstrom resolution. One of the beta-Q114 rotamer conformations allows a hydrogen bond to form with the PLP oxygen at the position 3 in the ring Deposited 2020-12-03	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–268（268 aa）	Not recorded	F9F 2-({[4-(TRIFLUOROMETHOXY)PHENYL]SULFONYL}AMINO)ETHYL DIHYDROGEN PHOSPHATE × 1 EDO 1,2-ETHANEDIOL × 5 CL CHLORIDE ION × 1 0JO 2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid × 1 BZI BENZIMIDAZOLE × 2 PEG DI(HYDROXYETHYL)ETHER × 1 PGE TRIETHYLENE GLYCOL × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；298 K；50 mM Bicine-CsOH, 9% PEG 8,000, 2 mM Spermine, pH 7.8	Resolution 1.51 Å R-free 0.231
7KYT The aminoacrylate form of the wild-type Salmonella typhimurium Tryptophan Synthase in complex with inhibitor N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the enzyme alpha-site, cesium ion at the metal coordination site and benzimidazole (BZI) at the enzyme beta-site at 1.35 Angstrom resolution Deposited 2020-12-08	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–268（268 aa）	Not recorded	F9F 2-({[4-(TRIFLUOROMETHOXY)PHENYL]SULFONYL}AMINO)ETHYL DIHYDROGEN PHOSPHATE × 1 EDO 1,2-ETHANEDIOL × 6 CS CESIUM ION × 2 0JO 2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid × 1 BZI BENZIMIDAZOLE × 2 BCN BICINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；298 K；50 mM Bicine-CsOH, 10% PEG 8,000, 2 mM Spermine, pH 7.8	Resolution 1.35 Å R-free 0.209
7L03 The aminoacrylate form of the wild-type Salmonella typhimurium Tryptophan Synthase in complex with inhibitor N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the enzyme alpha-site and sodium ion at the metal coordination site at 1.60 Angstrom resolution. Three water molecules are close to the amynoacrylate at the enzyme beta-site Deposited 2020-12-11	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–268（268 aa）	Not recorded	F9F 2-({[4-(TRIFLUOROMETHOXY)PHENYL]SULFONYL}AMINO)ETHYL DIHYDROGEN PHOSPHATE × 1 EDO 1,2-ETHANEDIOL × 6 0JO 2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid × 1 NA SODIUM ION × 1 PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；298 K；50 mM Bicine-CsOH, 10% PEG 8,000, 2 mM Spermine, pH 7.8	Resolution 1.60 Å R-free 0.224
7LEV The aminoacrylate form of the wild-type Salmonella typhimurium Tryptophan Synthase in complex with ammonium ion at the metal coordination site at 1.70 Angstrom resolution Deposited 2021-01-15	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–268（268 aa）	Not recorded	DMS DIMETHYL SULFOXIDE × 8 EDO 1,2-ETHANEDIOL × 3 CL CHLORIDE ION × 5 0JO 2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid × 1 NH4 AMMONIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；298 K；50 mM Bicine-CsOH, 10% PEG 8,000, 2 mM Spermine, pH 7.8	Resolution 1.70 Å R-free 0.246
7LKL The internal aldimine form of the wild-type Salmonella typhimurium Tryptophan Synthase in complex with inhibitor N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the enzyme alpha-site, cesium ion at the metal coordination site and the product L-tryptophan at the enzyme beta-site at 1.05 Angstrom resolution. One of the beta-Q114 rotamer conformations allows a hydrogen bond to form with the PLP oxygen at the position 3 in the ring Deposited 2021-02-02	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–268（268 aa）	Not recorded	F9F 2-({[4-(TRIFLUOROMETHOXY)PHENYL]SULFONYL}AMINO)ETHYL DIHYDROGEN PHOSPHATE × 2 DMS DIMETHYL SULFOXIDE × 26 TRP TRYPTOPHAN × 4 EDO 1,2-ETHANEDIOL × 18 CS CESIUM ION × 10 CL CHLORIDE ION × 8 PEG DI(HYDROXYETHYL)ETHER × 6 PLP PYRIDOXAL-5'-PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；298 K；50 mM Bicine-CsOH, 10% PEG 8,000, 2 mM Spermine, pH 7.8	Resolution 1.05 Å R-free 0.176
7MT4 Crystal structure of tryptophan Synthase in complex with F9, NH4+, pH7.8 - alpha aminoacrylate form - E(A-A) Deposited 2021-05-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–268（268 aa）	Not recorded	F9F 2-({[4-(TRIFLUOROMETHOXY)PHENYL]SULFONYL}AMINO)ETHYL DIHYDROGEN PHOSPHATE × 2 0JO 2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid × 2 NH4 AMMONIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；50 mM Bicine-NaOH pH 7.8, 10% PEG 8000, 2 mM spermine	Resolution 1.40 Å R-free 0.203
7MT5 Crystal structure of tryptophan synthase in complex with F9, Cs+, pH7.8 - alpha aminoacrylate form - E(A-A) Deposited 2021-05-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–268（268 aa）	Not recorded	F9F 2-({[4-(TRIFLUOROMETHOXY)PHENYL]SULFONYL}AMINO)ETHYL DIHYDROGEN PHOSPHATE × 2 0JO 2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid × 2 CS CESIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；50 mM Bicine-CsOH pH 7.8, 10% PEG 8000, 2 mM spermine	Resolution 1.50 Å R-free 0.208
7MT6 Crystal structure of tryptophan synthase in complex with F9, Cs+, benzimidazole, pH7.8 - alpha aminoacrylate form - E(A-A)(BZI) Deposited 2021-05-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–268（268 aa）	Not recorded	F9F 2-({[4-(TRIFLUOROMETHOXY)PHENYL]SULFONYL}AMINO)ETHYL DIHYDROGEN PHOSPHATE × 2 0JO 2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid × 2 CS CESIUM ION × 4 BZI BENZIMIDAZOLE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；50 mM Bicine-CsOH pH 7.8, 10% PEG 8000, 2 mM spermine	Resolution 1.70 Å R-free 0.193

18 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A0D6FWC1_SALTM
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–268； UniProt 1–268

Tryptophan synthase beta chain

Salmonella typhimurium

UniProt A0A0J0ZFZ1

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 1–397	Mutation：K167T	Tryptophan synthase alpha chain × 2 （A0A0D6FWC1） F9F 2-({[4-(TRIFLUOROMETHOXY)PHENYL]SULFONYL}AMINO)ETHYL DIHYDROGEN PHOSPHATE × 2 DMS DIMETHYL SULFOXIDE × 12 EDO 1,2-ETHANEDIOL × 6 CL CHLORIDE ION × 22 1D0 (2E)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)imino]-3-[(2-hydroxyphenyl)amino]propanoic acid × 2 2AP 2-AMINOPYRIDINE × 2 CS CESIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.9；297 K；50 mM Bicine-Cs, 10-12% PEG3350, 50 mM cesium chloride, 4-8 mM spermine	Resolution 1.79 Å R-free 0.232

Other States of the Same Protein in the Database

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	A0A0J0ZFZ1_SALTM
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–397； UniProt 1–397

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6duc
Deposition date deposition_date	2018-06-20
Structure title title	Crystal structure of mutant beta-K167T tryptophan synthase in complex with inhibitor N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the alpha-site, cesium ion at the metal coordination site, and 2-aminophenol quinonoid (1D0) at the beta-site
Keywords keywords	;F9F, 1D0, Cesium ion, mutant beta-K167T, lyase, lyase inhibitor, 2-aminophenol quinonoid, Salmonella typhimurium, LYASE-LYASE INHIBITOR complex ;; LYASE/LYASE INHIBITOR
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	27.28 Å
Radius of gyration Rg (electron density) rg_electron	26.47 Å
Forward intensity I(0) i0	86677600.00
Molecular weight molecular_weight	72397.0 kDa
Excluded volume excluded_volume	90046 Å³
Envelope volume envelope_volume	103420 Å³
Hydration-shell volume shell_volume	32595 Å³
Envelope diameter envelope_diameter	95.9 Å
Shell Rg shell_rg	33.99 Å
Envelope Rg envelope_rg	26.79 Å
Shape Rg shape_rg	26.40 Å
Total Rg total_rg	27.39 Å
Total atoms total_atoms	5034
Residues n_residues	660
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	91.8 Å
Rg (real space) rg_real	27.34 Å
Rg uncertainty (real space) rg_real_error	0.68 Å
I(0) (real space) i0_real	8.6680e+07
I(0) uncertainty (real space) i0_real_error	1.1110e+06
Rg (reciprocal space) rg_reciprocal	27.32 Å
I(0) (reciprocal space) i0_reciprocal	86680000.0000
Solution quality estimate total_estimate	0.8719
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.5 Å
Skewness Skewness skewness	0.449
Kurtosis Kurtosis kurtosis	-0.255
Angular range angular_range	— – 0.2900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	30930000.0000
Real-space data points n_real_points	59
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.795; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.962

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (10)

Entity 1 Entity 1 polymer

Description description	Tryptophan synthase alpha chain
Molecular weight formula_weight	28698.8 kDa
EC 编号 ec_number	4.2.1.20
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	5659

MERYENLFAQLNDRREGAFVPFVTLGDPGIEQSLKIIDTLIDAGADALELGVPFSDPLADGPTIQNANLRAFAAGVTPAQCFEMLALIREKHPTIPIGLLMYANLVFNNGIDAFYARCEQVGVDSVLVADVPVEESAPFRQAALRHNIAPIFICPPNADDDLLRQVASYGRGYTYLLSRSGVTGAENRGALPLHHLIEKLKEYHAAPALQGFGISSPEQVSAAVRAGAAGAISGSAIVKIIEKNLASPKQMLAELRSFVSAMKAASRA

来源 Source

来源生物 organism	Salmonella typhimurium
通用名 common_name	Salmonella enterica subsp. enterica serovar Typhimurium
NCBI Class编号 ncbi_taxonomy_id	90371
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Tryptophan synthase beta chain
Molecular weight formula_weight	42890.8 kDa
EC 编号 ec_number	4.2.1.20
Mutation mutation	K167T
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MTTLLNPYFGEFGGMYVPQILMPALNQLEEAFVSAQKDPEFQAQFADLLKNYAGRPTALTKCQNITAGTRTTLYLKREDLLHGGAHKTNQVLGQALLAKRMGKSEIIAETGAGQHGVASALASALLGLKCRIYMGAKDVERQSPNVFRMRLMGAEVIPVHSGSATLTDACNEALRDWSGSYETAHYMLGTAAGPHPYPTIVREFQRMIGEETKAQILDKEGRLPDAVIACVGGGSNAIGMFADFINDTSVGLIGVEPGGHGIETGEHGAPLKHGRVGIYFGMKAPMMQTADGQIEESYSISAGLDFPSVGPQHAYLNSIGRADYVSITDDEALEAFKTLCRHEGIIPALESSHALAHALKMMREQPEKEQLLVVNLSGRGDKDIFTVHDILKARGEI

来源 Source

来源生物 organism	Salmonella typhimurium
通用名 common_name	Salmonella enterica subsp. enterica serovar Typhimurium
NCBI Class编号 ncbi_taxonomy_id	90371
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	2-({[4-(TRIFLUOROMETHOXY)PHENYL]SULFONYL}AMINO)ETHYL DIHYDROGEN PHOSPHATE
Molecular weight formula_weight	365.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	DIMETHYL SULFOXIDE
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	11

Entity 7 Entity 7 non-polymer

Description description	(2E)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)imino]-3-[(2-hydroxyphenyl)amino]propanoic acid
Molecular weight formula_weight	425.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	2-AMINOPYRIDINE
Molecular weight formula_weight	95.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 non-polymer

Description description	CESIUM ION
Molecular weight formula_weight	132.9 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 10 Entity 10 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	519

▼

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d6duca_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.2 — Ribulose-phoshate binding barrel
Family Family family	c.1.2.4 — Tryptophan biosynthesis enzymes

Domain ID domain_id	d6ducb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.79 — Tryptophan synthase beta subunit-like PLP-dependent enzymes
Superfamily Superfamily superfamily	c.79.1 — Tryptophan synthase beta subunit-like PLP-dependent enzymes
Family Family family	c.79.1.1 — Tryptophan synthase beta subunit-like PLP-dependent enzymes

CATH v4.4 (3 domains)

Domain ID domain_id	6ducA00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	6ducB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1100 —

Domain ID domain_id	6ducB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1100 —

▶

8. Citations (1)

▶

Unit-cell length a length_a	184.261 Å
Unit-cell length b length_b	60.044 Å
Unit-cell length c length_c	67.298 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.65 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.791 Å
Low-resolution limit resolution_low	19.703 Å
R factor r_factor	0.1877
R_work r_work	0.1853
R_free r_free	0.2315

fit	/app/data/saxs_computation/du/6duc/6duc.fit
pddf	/app/data/pr_computation/du/6duc/6duc.pr.out
profile	/app/data/saxs_computation/du/6duc/6duc.dat

Crystal structure of mutant beta-K167T tryptophan synthase in complex with inhibitor N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the alpha-site, cesium ion at the metal coordination site, and 2-aminophenol quinonoid (1D0) at the beta-site

1. Protein Identity and Related Structures Protein Identity & Related Structures

Tryptophan synthase alpha chain

State in the Current Structure

Other States of the Same Protein in the Database

Tryptophan synthase beta chain

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (10)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 water

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)