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1njc

THYMIDYLATE SYNTHASE, MUTATION, N229D WITH 2'-DEOXYCYTIDINE 5'-MONOPHOSPHATE (DCMP)

Method: X-RAY DIFFRACTION Dmax: 65.8 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

THYMIDYLATE SYNTHASE

Lactobacillus casei

UniProt P00469

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 Mutation：N229D DCM 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 2 X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；pH 7.0 Resolution 2.50 Å

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 1NJC 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 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 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 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 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 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 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 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 mutation/modification Different ligand/ion Different experimental conditions 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 mutation/modification Different ligand/ion Different experimental conditions 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 mutation/modification Different ligand/ion Different experimental conditions 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 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
1NJD THYMIDYLATE SYNTHASE, MUTATION, N229D WITH 2'-DEOXYURIDINE 5'-MONOPHOSPHATE (DUMP) 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）
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 mutation/modification 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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–315（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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–315（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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–315（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 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）
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 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）
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 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）
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 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 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 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 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 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 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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–315（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 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）
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 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）
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
3BYX Lactobacillus CASEI Thymidylate Synthase Ternary Complex with DUMP and the Phtalimidic Derivative C00 in Multiple Binding Modes Deposited 2008-01-16 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）
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
3BZ0 Lactobacillus Casei Thymidylate Synthase Ternary Complex with DUMP and the Phtalimidic Derivative C00 Deposited 2008-01-17 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）
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 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）
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 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）
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 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）
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 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）
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 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）
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 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）
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

SAXS profile for 1njc

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1njc
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1njc
Deposition date deposition_date1996-01-23
Structure title titleTHYMIDYLATE SYNTHASE, MUTATION, N229D WITH 2'-DEOXYCYTIDINE 5'-MONOPHOSPHATE (DCMP)
Keywords keywordsTRANSFERASE, METHYLTRANSFERASE, NUCLEOTIDE BIOSYNTHESIS, TRANSFERASE (METHYLTRANSFERASE); TRANSFERASE (METHYLTRANSFERASE)
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier21.55 Å
Radius of gyration Rg (electron density) rg_electron20.19 Å
Forward intensity I(0) i022631900.00
Molecular weight molecular_weight36875.0 kDa
Excluded volume excluded_volume46316 ų
Envelope volume envelope_volume54783 ų
Hydration-shell volume shell_volume22513 ų
Envelope diameter envelope_diameter66.2 Å
Shell Rg shell_rg26.89 Å
Envelope Rg envelope_rg20.26 Å
Shape Rg shape_rg20.17 Å
Total Rg total_rg21.13 Å
Total atoms total_atoms2613
Residues n_residues316
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax65.8 Å
Rg (real space) rg_real21.39 Å
Rg uncertainty (real space) rg_real_error0.34 Å
I(0) (real space) i0_real2.2630e+07
I(0) uncertainty (real space) i0_real_error2.6760e+05
Rg (reciprocal space) rg_reciprocal21.42 Å
I(0) (reciprocal space) i0_reciprocal22630000.0000
Solution quality estimate total_estimate0.9069
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.1 Å
Skewness Skewness skewness0.101
Kurtosis Kurtosis kurtosis-0.472
Angular range angular_range— – 0.3700 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3241000.0000
Real-space data points n_real_points69
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.933; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.996
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1njca_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.117 — Thymidylate synthase/dCMP hydroxymethylase
Superfamily Superfamily superfamilyd.117.1 — Thymidylate synthase/dCMP hydroxymethylase
Family Family familyd.117.1.1 — Thymidylate synthase/dCMP hydroxymethylase

CATH v4.4 (1 domains)

Domain ID domain_id1njcA00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology572 — Thymidylate Synthase; Chain A
Homologous superfamily homologous superfamily10 — Thymidylate synthase/dCMP hydroxymethylase domain
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8. Citations (5)

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9. Files and Curves (10)