3byx

Lactobacillus CASEI Thymidylate Synthase Ternary Complex with DUMP and the Phtalimidic Derivative C00 in Multiple Binding Modes

Method: X-RAY DIFFRACTION D_max: 66.4 Å Quality: EXCELLENT

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

Thymidylate synthase

Lactobacillus casei

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–316	Not recorded	UMP 2'-DEOXYURIDINE 5'-MONOPHOSPHATE × 2 C00 2-(4-hydroxybiphenyl-3-yl)-4-methyl-1H-isoindole-1,3(2H)-dione × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；1mM EDTA, 100mM ammonium phosphate, 5% (v/v) PEG 400, 20mM Tris-HCl, DMSO, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.40 Å R-free 0.283

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 3BYX	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BO7 THYMIDYLATE SYNTHASE R179T MUTANT Deposited 1998-08-10	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–316（316 aa）	Mutation：R179T	U5P URIDINE-5'-MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.0	Resolution 2.40 Å R-free 0.276
1BO8 THYMIDYLATE SYNTHASE R178T MUTANT Deposited 1998-08-10	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–316（316 aa）	Mutation：R178T	K POTASSIUM ION × 2 U5P URIDINE-5'-MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.0	Resolution 2.40 Å R-free 0.273
1BP0 THYMIDYLATE SYNTHASE R23I MUTANT Deposited 1998-08-11	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–316（316 aa）	Mutation：R23I	K POTASSIUM ION × 2 UMP 2'-DEOXYURIDINE 5'-MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.0	Resolution 2.40 Å R-free 0.279
1BP6 THYMIDYLATE SYNTHASE R23I, R179T DOUBLE MUTANT Deposited 1998-08-13	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–316（316 aa）	Mutation：R23I, R179T	K POTASSIUM ION × 2 UMP 2'-DEOXYURIDINE 5'-MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.0	Resolution 2.40 Å R-free 0.271
1BP6 THYMIDYLATE SYNTHASE R23I, R179T DOUBLE MUTANT Deposited 1998-08-13	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–316（316 aa）	Mutation：R23I, R179T	K POTASSIUM ION × 2 UMP 2'-DEOXYURIDINE 5'-MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.0	Resolution 2.40 Å R-free 0.271
1BPJ THYMIDYLATE SYNTHASE R178T, R179T DOUBLE MUTANT Deposited 1998-08-11	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–316（316 aa）	Mutation：R178T, R179T	K POTASSIUM ION × 2 UMP 2'-DEOXYURIDINE 5'-MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.0	Resolution 2.40 Å R-free 0.281
1BPJ THYMIDYLATE SYNTHASE R178T, R179T DOUBLE MUTANT Deposited 1998-08-11	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–316（316 aa）	Mutation：R178T, R179T	K POTASSIUM ION × 2 UMP 2'-DEOXYURIDINE 5'-MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.0	Resolution 2.40 Å R-free 0.281
1JMF CONTRIBUTIONS OF ORIENTATION AND HYDROGEN BONDING TO CATALYSIS IN ASN-229 MUTANTS OF THYMIDYLATE SYNTHASE Deposited 1997-09-13	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–316（316 aa）	Mutation：N229A	UMP 2'-DEOXYURIDINE 5'-MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；pH 7.4	Resolution 2.50 Å R-free 0.270
1JMG CONTRIBUTIONS OF ORIENTATION AND HYDROGEN BONDING TO CATALYSIS IN ASN-229 MUTANTS OF THYMIDYLATE SYNTHASE Deposited 1997-09-13	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–316（316 aa）	Mutation：N229G	UMP 2'-DEOXYURIDINE 5'-MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；pH 7.4	Resolution 2.20 Å R-free 0.271
1JMH CONTRIBUTIONS OF ORIENTATION AND HYDROGEN BONDING TO CATALYSIS IN ASN-229 MUTANTS OF THYMIDYLATE SYNTHASE Deposited 1997-09-13	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–316（316 aa）	Mutation：N229I	UMP 2'-DEOXYURIDINE 5'-MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；pH 7.4	Resolution 2.50 Å R-free 0.311
1JMI CONTRIBUTIONS OF ORIENTATION AND HYDROGEN BONDING TO CATALYSIS IN ASN-229 MUTANTS OF THYMIDYLATE SYNTHASE Deposited 1997-09-13	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–316（316 aa）	Mutation：N229S	UMP 2'-DEOXYURIDINE 5'-MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；pH 7.4	Resolution 2.50 Å R-free 0.262
1LCA LACTOBACILLUS CASEI THYMIDYLATE SYNTHASE TERNARY COMPLEX WITH DUMP AND CB3717 Deposited 1995-06-22	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–316（316 aa）	Not recorded	UMP 2'-DEOXYURIDINE 5'-MONOPHOSPHATE × 2 CB3 10-PROPARGYL-5,8-DIDEAZAFOLIC ACID × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
1LCB LACTOBACILLUS CASEI THYMIDYLATE SYNTHASE TERNARY COMPLEX WITH DTMP AND H2FOLATE Deposited 1995-06-22	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–316（316 aa）	Not recorded	TMP THYMIDINE-5'-PHOSPHATE × 2 DHF DIHYDROFOLIC ACID × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
1LCE LACTOBACILLUS CASEI THYMIDYLATE SYNTHASE TERNARY COMPLEX WITH DUMP AND CH2THF Deposited 1995-06-22	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–316（316 aa）	Not recorded	UMP 2'-DEOXYURIDINE 5'-MONOPHOSPHATE × 2 TMF 5,10-METHYLENE-6-HYDROFOLIC ACID × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
1NJA THYMIDYLATE SYNTHASE, MUTATION, N229C WITH 2'-DEOXYCYTIDINE 5'-MONOPHOSPHATE (DCMP) Deposited 1996-01-23	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–316（316 aa）	Mutation：N229C	DCM 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.0	Resolution 2.50 Å
1NJB THYMIDYLATE SYNTHASE Deposited 1996-01-23	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–316（316 aa）	Mutation：N229C	UMP 2'-DEOXYURIDINE 5'-MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；pH 7.4	Resolution 2.74 Å
1NJC THYMIDYLATE SYNTHASE, MUTATION, N229D WITH 2'-DEOXYCYTIDINE 5'-MONOPHOSPHATE (DCMP) Deposited 1996-01-23	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–316（316 aa）	Mutation：N229D	DCM 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.0	Resolution 2.50 Å
1NJD THYMIDYLATE SYNTHASE, MUTATION, N229D WITH 2'-DEOXYURIDINE 5'-MONOPHOSPHATE (DUMP) Deposited 1996-01-23	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–316（316 aa）	Mutation：N229D	UMP 2'-DEOXYURIDINE 5'-MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；pH 7.4	Resolution 2.20 Å
1NJE THYMIDYLATE SYNTHASE WITH 2'-DEOXYCYTIDINE 5'-MONOPHOSPHATE (DCMP) Deposited 1996-01-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–316（316 aa）	Not recorded	DCM 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；pH 7.4	Resolution 2.30 Å
1TDA STRUCTURES OF THYMIDYLATE SYNTHASE WITH A C-TERMINAL DELETION: ROLE OF THE C-TERMINUS IN ALIGNMENT OF D/UMP AND CH2H4FOLATE Deposited 1993-02-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–315（315 aa）	Not recorded	PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.09 Å
1TDB STRUCTURES OF THYMIDYLATE SYNTHASE WITH A C-TERMINAL DELETION: ROLE OF THE C-TERMINUS IN ALIGNMENT OF D/UMP AND CH2H4FOLATE Deposited 1993-02-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–315（315 aa）	Not recorded	UFP 5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.65 Å
1TDC STRUCTURES OF THYMIDYLATE SYNTHASE WITH A C-TERMINAL DELETION: ROLE OF THE C-TERMINUS IN ALIGNMENT OF D/UMP AND CH2H4FOLATE Deposited 1993-02-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–315（315 aa）	Not recorded	UMP 2'-DEOXYURIDINE 5'-MONOPHOSPHATE × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.65 Å
1THY REFINED STRUCTURES OF SUBSTRATE-BOUND AND PHOSPHATE-BOUND THYMIDYLATE SYNTHASE FROM LACTOBACILLUS CASEI Deposited 1993-04-02	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–316（316 aa）	Not recorded	UMP 2'-DEOXYURIDINE 5'-MONOPHOSPHATE × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.90 Å
1TSL L. CASEI THYMIDYLATE SYNTHASE WITH SPECIES SPECIFIC INHIBITOR Deposited 1997-06-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–316（316 aa）	Not recorded	PO4 PHOSPHATE ION × 2 A15 3'-3"-DICHLOROPHENOL-1,8-3H-BENZO[DE]ISOCHROMEN-1-ONE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；6 MG/ML PROTEIN, PH 7.4; 1% AMMONIUM SULFATE, 1 MM DTT, + 1 % SATURATED LIGAND-DMSO SOLUTION. HANGING DROP OVER 20 MM KPO4, PH 6.8 AND 1 MM DTT., vapor diffusion - hanging drop	Resolution 2.50 Å R-free 0.251
1TSM L. CASEI THYMIDYLATE SYNTHASE WITH SPECIES SPECIFIC INHIBITOR Deposited 1997-06-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–316（316 aa）	Not recorded	PO4 PHOSPHATE ION × 2 MR2 3-DIPHENOL-6-NITRO-3H-BENZO[DE]ISOCHROMEN-1-ONE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；6 MG/ML PROTEIN, PH 7.4; 1% AMMONIUM SULFATE, 1 MM DTT, + 1 % SATURATED LIGAND-DMSO SOLUTION. HANGING DROP OVER 20 MM KPO4, PH 6.8 AND 1 MM DTT., vapor diffusion - hanging drop	Resolution 3.00 Å R-free 0.222
1TSV THYMIDYLATE SYNTHASE R179A MUTANT Deposited 1995-12-05	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–316（316 aa）	Mutation：R179A	UMP 2'-DEOXYURIDINE 5'-MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；pH 7.4	Resolution 2.90 Å
1TSW THYMIDYLATE SYNTHASE R179A MUTANT Deposited 1995-12-05	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–316（316 aa）	Mutation：R179A	PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；pH 7.4	Resolution 2.50 Å
1TSX THYMIDYLATE SYNTHASE R179E MUTANT Deposited 1995-12-05	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–316（316 aa）	Mutation：R179E	UMP 2'-DEOXYURIDINE 5'-MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；pH 7.4	Resolution 2.50 Å
1TSY THYMIDYLATE SYNTHASE R179K MUTANT Deposited 1995-12-05	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–316（316 aa）	Mutation：R179K	UMP 2'-DEOXYURIDINE 5'-MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.2；pH 7.2	Resolution 2.20 Å
1TSZ THYMIDYLATE SYNTHASE R179K MUTANT Deposited 1995-12-05	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–316（316 aa）	Mutation：R179K	PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.75 Å
1TVU CONTRIBUTIONS OF ORIENTATION AND HYDROGEN BONDING TO CATALYSIS IN ASN-229 MUTANTS OF THYMIDYLATE SYNTHASE Deposited 1997-09-17	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–316（316 aa）	Mutation：N229A	UMP 2'-DEOXYURIDINE 5'-MONOPHOSPHATE × 2 CB3 10-PROPARGYL-5,8-DIDEAZAFOLIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；pH 7.4	Resolution 2.50 Å R-free 0.308
1TVV CONTRIBUTIONS OF ORIENTATION AND HYDROGEN BONDING TO CATALYSIS IN ASN-229 MUTANTS OF THYMIDYLATE SYNTHASE Deposited 1997-09-17	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–316（316 aa）	Mutation：N229C	UMP 2'-DEOXYURIDINE 5'-MONOPHOSPHATE × 2 CB3 10-PROPARGYL-5,8-DIDEAZAFOLIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 2.30 Å R-free 0.283
1TVW CONTRIBUTIONS OF ORIENTATION AND HYDROGEN BONDING TO CATALYSIS IN ASN-229 MUTANTS OF THYMIDYLATE SYNTHASE Deposited 1997-09-17	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–316（316 aa）	Mutation：N229S	UMP 2'-DEOXYURIDINE 5'-MONOPHOSPHATE × 2 CB3 10-PROPARGYL-5,8-DIDEAZAFOLIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；pH 7.4	Resolution 2.50 Å R-free 0.314
1VZA THYMIDYLATE SYNTHASE E60D MUTANT BINARY COMPLEX WITH 2'-DEOXYURIDINE 5'-MONOPHOSPHATE (DUMP) Deposited 1996-09-18	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–316（316 aa）	Mutation：E60D	UMP 2'-DEOXYURIDINE 5'-MONOPHOSPHATE × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
1VZB L. CASEI THYMIDYLATE SYNTHASE MUTANT E60Q BINARY COMPLEX WITH DUMP Deposited 1996-09-18	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–316（316 aa）	Mutation：E60Q	UMP 2'-DEOXYURIDINE 5'-MONOPHOSPHATE × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
1VZC L. CASEI THYMIDYLATE SYNTHASE MUTANT E60Q BINARY COMPLEX WITH FDUMP Deposited 1996-09-18	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–316（316 aa）	Mutation：E60Q	UFP 5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
1VZD L. CASEI THYMIDYLATE SYNTHASE MUTANT E60Q TERNARY COMPLEX WITH FDUMP AND CB3717 Deposited 1996-09-18	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–316（316 aa）	Mutation：E60Q	UFP 5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE × 2 CB3 10-PROPARGYL-5,8-DIDEAZAFOLIC ACID × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
1VZE L. CASEI THYMIDYLATE SYNTHASE MUTANT E60Q TERNARY COMPLEX WITH DUMP AND CB3717 Deposited 1996-09-18	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–316（316 aa）	Mutation：E60Q	UMP 2'-DEOXYURIDINE 5'-MONOPHOSPHATE × 2 CB3 10-PROPARGYL-5,8-DIDEAZAFOLIC ACID × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å
2G86 L. casei thymidylate synthase Y261F in complex with substrate, dUMP Deposited 2006-03-01	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–316（316 aa）	Mutation：Y261F	UMP 2'-DEOXYURIDINE 5'-MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；vapor diffusion against 20mM KPO4 buffer; protein solution in same buffer with 15-20mM ammonium sulfate, DTT, 38 mMdUMP, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.40 Å R-free 0.233
2G89 L. casei thymidylate synthase Y261A in complex with substrate, dUMP Deposited 2006-03-02	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–316（316 aa）	Mutation：Y261A	UMP 2'-DEOXYURIDINE 5'-MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；protein in 20mM KPO4 buffer with 15-20mM ammonium sulfate, DTT and 38mM dUMP, against 20mM KPO4 buffer alone, VAPOR DIFFUSION, HANGING DROP, temperature 295K, pH 7.00	Resolution 2.50 Å R-free 0.248
2G8A Lactobacillus casei Y261M in complex with substrate, dUMP Deposited 2006-03-02	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–316（316 aa）	Mutation：Y261M	UMP 2'-DEOXYURIDINE 5'-MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；Vapor diffusion against 20 mM KPO4 from protein solutions in the same buffer with 15-20 mM ammonium sulfate, DTT, and 38mM dUMP, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.40 Å R-free 0.276
2G8D Lactobacillus casei thymidylate synthase Y261W-dUMP complex Deposited 2006-03-02	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–316（316 aa）	Mutation：Y261W	UMP 2'-DEOXYURIDINE 5'-MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；Vapor diffusion against 20mM KPO4 buffer from protein solutions in the same buffer, containing 15-20mM ammonium sulfate, DTT and 38mM dUMP, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295.K	Resolution 2.40 Å R-free 0.251
2TDD STRUCTURES OF THYMIDYLATE SYNTHASE WITH A C-TERMINAL DELETION: ROLE OF THE C-TERMINUS IN ALIGNMENT OF D/UMP AND CH2H4FOLATE Deposited 1993-04-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–315（315 aa）	Not recorded	THF 5-HYDROXYMETHYLENE-6-HYDROFOLIC ACID × 2 UFP 5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.70 Å
2TDM STRUCTURE OF THYMIDYLATE SYNTHASE Deposited 1997-03-28	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–316（316 aa）	Not recorded	UMP 2'-DEOXYURIDINE 5'-MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；pH 7.4	Resolution 2.55 Å
3BNZ Crystal structure of Thymidylate Synthase ternary complex with dUMP and 8A inhibitor Deposited 2007-12-15	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–316（316 aa）	Not recorded	PO4 PHOSPHATE ION × 2 UMP 2'-DEOXYURIDINE 5'-MONOPHOSPHATE × 2 C16 4-(4-methyl-1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)benzonitrile × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；100mM (NH4)H2PO4/(NH4)2HPO4, 5% v/v PEG 400, 20mM Tris-HCl buffer pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.60 Å R-free 0.323
3BZ0 Lactobacillus Casei Thymidylate Synthase Ternary Complex with DUMP and the Phtalimidic Derivative C00 Deposited 2008-01-17	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–316（316 aa）	Not recorded	UMP 2'-DEOXYURIDINE 5'-MONOPHOSPHATE × 2 C00 2-(4-hydroxybiphenyl-3-yl)-4-methyl-1H-isoindole-1,3(2H)-dione × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；1mM EDTA, 20 mM Tris-HCl, dUMP, 100mM ammonium phopshate, 5% (v/v) PEG 400, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.70 Å R-free 0.326
3C06 Lactobacillus CASEI Thymidylate Synthase Ternary Complex With DUMP and the Phtalimidic Derivative 14C in Multiple Binding Modes-Mode 1 Deposited 2008-01-18	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–316（316 aa）	Not recorded	UMP 2'-DEOXYURIDINE 5'-MONOPHOSPHATE × 2 14C 2-(2-chloropyridin-4-yl)-4-methyl-1H-isoindole-1,3(2H)-dione × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；4mg/mL LcTS, 1mM EDTA, 40mM dUMP, 20mM TRIS HCl, 100mM ammonium phosphate, 5% PEG 400 (v/v), 10-12% ligand solution in DMSO, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.60 Å R-free 0.292
3C0A Lactobacillus CASEI Thymidylate Synthase Ternary Complex with DUMP and the Phtalimidic Derivative 14C in Multiple Binding Modes-Mode 2 Deposited 2008-01-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–316（316 aa）	Not recorded	UMP 2'-DEOXYURIDINE 5'-MONOPHOSPHATE × 2 14C 2-(2-chloropyridin-4-yl)-4-methyl-1H-isoindole-1,3(2H)-dione × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；4mg/mL LcTS, 1mM EDTA, 40mM dUMP, 20mM TRIS HCl,100mM ammonium phosphate, 5% PEG 400 v/v, 10-12% ligand solution in DMSO, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.40 Å R-free 0.326
3IJZ Lactobacillus casei Thymidylate Synthase ternary complex with dUMP and Pthalimidic derivative 15C Deposited 2009-08-05	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–316（316 aa）	Not recorded	15C 2-(4-acetylphenyl)-4-methyl-1H-isoindole-1,3(2H)-dione × 2 UMP 2'-DEOXYURIDINE 5'-MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；298 K；10% saturated Ammonium sulfate, 1mM DTT, 20mM Potassium phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.21 Å R-free 0.253
3IK0 Lactobacillus casei Thymidylate Synthase in Ternary Complex with dUMP and the Phtalimidic Derivative 7C1 Deposited 2009-08-05	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–316（316 aa）	Not recorded	7C1 4-(4-methyl-1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)benzenecarboximidamide × 2 UMP 2'-DEOXYURIDINE 5'-MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；298 K；10% saturated Ammonium sulfate, 1mM DTT, 20mM Potassium phosphate , pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.10 Å R-free 0.258
3IK1 Lactobacillus casei Thymidylate Synthase in Ternary Complex with dUMP and the Phtalimidic Derivative 20C Deposited 2009-08-05	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–316（316 aa）	Not recorded	20C 2-hydroxy-4-(4-methyl-1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)benzoic acid × 2 UMP 2'-DEOXYURIDINE 5'-MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；298 K；10% saturated Ammonium sulfate, 1mM DTT, 20mM Potassium phosphate , pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.25 Å R-free 0.271
4TMS PLASTIC ADAPTATION TOWARD MUTATIONS IN PROTEINS: STRUCTURAL COMPARISON OF THYMIDYLATE SYNTHASES Deposited 1992-01-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–316（316 aa）	Not recorded	PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.35 Å

50 other PDB entries and 52 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TYSY_LACCA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–316； UniProt 1–316

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	3byx
Deposition date deposition_date	2008-01-16
Structure title title	Lactobacillus CASEI Thymidylate Synthase Ternary Complex with DUMP and the Phtalimidic Derivative C00 in Multiple Binding Modes
Keywords keywords	Structure Based Drug Design, Methyltransferase, Nucleotide biosynthesis, Transferase; TRANSFERASE
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	21.25 Å
Radius of gyration Rg (electron density) rg_electron	19.87 Å
Forward intensity I(0) i0	22424000.00
Molecular weight molecular_weight	36846.0 kDa
Excluded volume excluded_volume	46325 Å³
Envelope volume envelope_volume	53795 Å³
Hydration-shell volume shell_volume	22329 Å³
Envelope diameter envelope_diameter	67.9 Å
Shell Rg shell_rg	26.63 Å
Envelope Rg envelope_rg	20.10 Å
Shape Rg shape_rg	19.85 Å
Total Rg total_rg	20.84 Å
Total atoms total_atoms	2613
Residues n_residues	313
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	66.4 Å
Rg (real space) rg_real	21.10 Å
Rg uncertainty (real space) rg_real_error	0.36 Å
I(0) (real space) i0_real	2.2420e+07
I(0) uncertainty (real space) i0_real_error	2.8610e+05
Rg (reciprocal space) rg_reciprocal	21.13 Å
I(0) (reciprocal space) i0_reciprocal	22420000.0000
Solution quality estimate total_estimate	0.9003
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.4 Å
Skewness Skewness skewness	0.112
Kurtosis Kurtosis kurtosis	-0.460
Angular range angular_range	— – 0.3750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3642000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.907; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.987

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Thymidylate synthase
Molecular weight formula_weight	36630.5 kDa
EC 编号 ec_number	2.1.1.45
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	2761

MLEQPYLDLAKKVLDEGHFKPDRTHTGTYSIFGHQMRFDLSKGFPLLTTKKVPFGLIKSELLWFLHGDTNIRFLLQHRNHIWDEWAFEKWVKSDEYHGPDMTDFGHRSQKDPEFAAVYHEEMAKFDDRVLHDDAFAAKYGDLGLVYGSQWRAWHTSKGDTIDQLGDVIEQIKTHPYSRRLIVSAWNPEDVPTMALPPCHTLYQFYVNDGKLSLQLYQRSADIFLGVPFNIASYALLTHLVAHECGLEVGEFIHTFGDAHLYVNHLDQIKEQLSRTPRPAPTLQLNPDKHDIFDFDMKDIKLLNYDPYPAIKAPVAV

来源 Source

来源生物 organism	Lactobacillus casei
NCBI Class编号 ncbi_taxonomy_id	1582
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	;2'-DEOXYURIDINE 5'-MONOPHOSPHATE ;
Molecular weight formula_weight	308.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	2-(4-hydroxybiphenyl-3-yl)-4-methyl-1H-isoindole-1,3(2H)-dione
Molecular weight formula_weight	329.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	123

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3byxa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.117 — Thymidylate synthase/dCMP hydroxymethylase
Superfamily Superfamily superfamily	d.117.1 — Thymidylate synthase/dCMP hydroxymethylase
Family Family family	d.117.1.1 — Thymidylate synthase/dCMP hydroxymethylase

CATH v4.4 (1 domains)

Domain ID domain_id	3byxA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	572 — Thymidylate Synthase; Chain A
Homologous superfamily homologous superfamily	10 — Thymidylate synthase/dCMP hydroxymethylase domain

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8. Citations (1)

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Unit-cell length a length_a	77.012 Å
Unit-cell length b length_b	77.012 Å
Unit-cell length c length_c	213.970 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	48.740 Å
R factor r_factor	0.2080
R_work r_work	0.2040
R_free r_free	0.2830

fit	/app/data/saxs_computation/by/3byx/3byx.fit
pddf	/app/data/pr_computation/by/3byx/3byx.pr.out
profile	/app/data/saxs_computation/by/3byx/3byx.dat