1jtu

E. coli Thymidylate Synthase in a Complex with dUMP and LY338913, A Polyglutamylated Pyrrolo(2,3-d)pyrimidine-based Antifolate

Method: X-RAY DIFFRACTION Dmax: 76.3 Å Quality: GOOD

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

THYMIDYLATE SYNTHASE

Escherichia coli

UniProt P0A884

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) UMP 2'-DEOXYURIDINE 5'-MONOPHOSPHATE × 2 LYB 2-{4-[4-(4-{4-[2-(2-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3-D]PYRIMIDIN-5-YL)-ETHYL]-BENZOYLAMINO}-4-CARBOXY-BUTYRYLAMIN O)-4-CARBOXY-BUTYRYLAMINO}-PENTANEDIOIC ACID × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;296 K;potassium phosphate, MgCl2, ammonium sulfate, DTT, EDTA, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K Resolution 2.20 Å R-free 0.241

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.

56 other PDB entries and 63 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 1–264; UniProt 1–264 Author chain B; PDBConstruct 1–264; 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 1jtu

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1jtu
Deposition date deposition_date2001-08-22
Structure title titleE. coli Thymidylate Synthase in a Complex with dUMP and LY338913, A Polyglutamylated Pyrrolo(2,3-d)pyrimidine-based Antifolate
Keywords keywordsantifolate, dTMP synthesis, cancer, drug resistance, polyglutamylation, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier24.43
Radius of gyration Rg (electron density) rg_electron23.11
Forward intensity I(0) i066117500.00
Molecular weight molecular_weight63015.0 kDa
Excluded volume excluded_volume78443 ų
Envelope volume envelope_volume89389 ų
Hydration-shell volume shell_volume30964 ų
Envelope diameter envelope_diameter79.0
Shell Rg shell_rg31.46
Envelope Rg envelope_rg23.38
Shape Rg shape_rg23.10
Total Rg total_rg24.00
Total atoms total_atoms4444
Residues n_residues526
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

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

Maximum dimension Dmax dmax76.3
Rg (real space) rg_real24.28
Rg uncertainty (real space) rg_real_error0.38
I(0) (real space) i0_real6.6120e+07
I(0) uncertainty (real space) i0_real_error9.0760e+05
Rg (reciprocal space) rg_reciprocal24.31
I(0) (reciprocal space) i0_reciprocal66120000.0000
Solution quality estimate total_estimate0.8975
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary73.9
Skewness Skewness skewness0.201
Kurtosis Kurtosis kurtosis-0.381
Angular range angular_range— – 0.3250 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha16540000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.893; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.992

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1jtua_
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_idd1jtub_
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_id1jtuA00
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_id1jtuB00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology572 — Thymidylate Synthase; Chain A
Homologous superfamily homologous superfamily10 — Thymidylate synthase/dCMP hydroxymethylase domain

8. Citations (3)

9. Files and Curves (10)