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1tsd

THYMIDYLATE SYNTHASE COMPLEX WITH 2'-DEOXYURIDINE 5'-MONOPHOSPHATE (DUMP) AND FOLATE ANALOG 1843U89

Method: X-RAY DIFFRACTION Dmax: 73.8 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

THYMIDYLATE SYNTHASE

Escherichia coli

UniProt P00470

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 1–264 Chain B； UniProt 1–264 Non-standard monomer：Yes (specific site not provided by mmCIF) BME BETA-MERCAPTOETHANOL × 2 UMP 2'-DEOXYURIDINE 5'-MONOPHOSPHATE × 2 F89 S)-2-(5(((1,2-DIHYDRO-3-METHYL-1-OXOBENZO(F)QUINAZOLIN-9-YL)METHYL)AMINO)1-OXO-2-ISOINDOLINYL)GLUTARIC ACID × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 1.95 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 1TSD Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BDU E. COLI THYMIDYLATE SYNTHASE COMPLEXED WITH DURD Deposited 1997-06-27 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 1–264（264 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) PO4 PHOSPHATE ION × 2 DUR 2'-DEOXYURIDINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；CRYSTALLIZATION EXPERIMENTS WERE CONDUCTED IN HANGING DROPS CONTAINING 4.2 MG/ML E. COLI TS, 0.38 MM DURD, 3.8 MM DTT, AND 1.2 M (NH4)2SO4, AT PH 7.8 (20 MM KPO4) SUSPENDED OVER A WELL SOLUTION CONTAINING 2.4 M (NH4)2SO4 AND 1.0 MM DTT., vapor diffusion - hanging drop
Resolution 2.10 Å R-free 0.237
1TJS E. COLI THYMIDYLATE SYNTHASE Deposited 1997-06-27 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 1–264（264 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；CRYSTALLIZATION EXPERIMENTS WERE CONDUCTED IN HANGING DROPS CONTAINING 4.2 MG/ML E. COLI TS, 3.8 MM DTT, AND 1.2 M (NH4)2SO4, AT PH 7.8 (20 MM KPO4) SUSPENDED OVER A WELL SOLUTION CONTAINING 2.4 M (NH4)2SO4 AND 1.0 MM DTT., vapor diffusion - hanging drop
Resolution 2.20 Å R-free 0.253
1TLC THYMIDYLATE SYNTHASE COMPLEXED WITH DGMP AND FOLATE ANALOG 1843U89 Deposited 1995-03-07 Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–264（264 aa）
Chain B 1–264（264 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) DGP 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE × 2 F89 S)-2-(5(((1,2-DIHYDRO-3-METHYL-1-OXOBENZO(F)QUINAZOLIN-9-YL)METHYL)AMINO)1-OXO-2-ISOINDOLINYL)GLUTARIC ACID × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.10 Å
1TLS THYMIDYLATE SYNTHASE TERNARY COMPLEX WITH FDUMP AND METHYLENETETRAHYDROFOLATE Deposited 1996-12-03 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–264（263 aa）
Chain B 2–264（263 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) UFP 5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE × 2 C2F 5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；CRYSTALLIZED BY VAPOR DIFFUSION FROM A SOLUTION OF 8MG/ML PROTEIN, 2MM FDUMP, 10MM CH2THF, 20MM PHOSPHATE PH 7.5, 4MM DTT, AND 1.05M AMMONIUM SULFATE; EQUILIBRATED AGAINST A SOLUTION OF 2.10M AMMONIUM SULFATE, 20MM PHOSPHATE PH 7.5, AND 4MM DTT., vapor diffusion
Resolution 2.60 Å
1TSN THYMIDYLATE SYNTHASE TERNARY COMPLEX WITH FDUMP AND METHYLENETETRAHYDROFOLATE Deposited 1996-12-02 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 2–264（263 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) PO4 PHOSPHATE ION × 2 UFP 5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE × 2 C2F 5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8；CRYSTALLIZED BY VAPOR DIFFUSION FROM A SOLUTION OF 8MG/ML PROTEIN, 2MM FDUMP, 10MM CH2THF, 20MM PHOSPHATE PH 8.0, 4MM DTT, AND 1.05M AMMONIUM SULFATE; EQUILIBRATED AGAINST A SOLUTION OF 2.10M AMMONIUM SULFATE, 20MM PHOSPHATE PH 8.0, AND 4MM DTT., vapor diffusion
Resolution 2.20 Å
1TYS WATER-MEDIATED SUBSTRATE(SLASH)PRODUCT DISCRIMINATION: THE PRODUCT COMPLEX OF THYMIDYLATE SYNTHASE AT 1.83 ANGSTROMS Deposited 1993-05-07 Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–264（264 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) TMP THYMIDINE-5'-PHOSPHATE × 2 DHF DIHYDROFOLIC ACID × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.80 Å

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TYSY_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–265； UniProt 1–264 Author chain B； PDBConstruct 2–265； UniProt 1–264

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 1tsd

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1tsd
Deposition date deposition_date1995-08-15
Structure title titleTHYMIDYLATE SYNTHASE COMPLEX WITH 2'-DEOXYURIDINE 5'-MONOPHOSPHATE (DUMP) AND FOLATE ANALOG 1843U89
Keywords keywordsDUMP, 1843U89, 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_guinier24.39 Å
Radius of gyration Rg (electron density) rg_electron23.05 Å
Forward intensity I(0) i065358600.00
Molecular weight molecular_weight62805.0 kDa
Excluded volume excluded_volume78313 ų
Envelope volume envelope_volume88493 ų
Hydration-shell volume shell_volume30783 ų
Envelope diameter envelope_diameter74.3 Å
Shell Rg shell_rg31.34 Å
Envelope Rg envelope_rg23.26 Å
Shape Rg shape_rg23.04 Å
Total Rg total_rg23.96 Å
Total atoms total_atoms4428
Residues n_residues528
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 dmax73.8 Å
Rg (real space) rg_real24.23 Å
Rg uncertainty (real space) rg_real_error0.33 Å
I(0) (real space) i0_real6.5360e+07
I(0) uncertainty (real space) i0_real_error8.4480e+05
Rg (reciprocal space) rg_reciprocal24.27 Å
I(0) (reciprocal space) i0_reciprocal65360000.0000
Solution quality estimate total_estimate0.9045
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary31.6 Å
Skewness Skewness skewness0.182
Kurtosis Kurtosis kurtosis-0.400
Angular range angular_range— – 0.3250 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha15470000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.930; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.978
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1tsda_
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
Domain ID domain_idd1tsdb_
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 (2 domains)

Domain ID domain_id1tsdA00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology572 — Thymidylate Synthase; Chain A
Homologous superfamily homologous superfamily10 — Thymidylate synthase/dCMP hydroxymethylase domain
Domain ID domain_id1tsdB00
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 (3)

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9. Files and Curves (10)