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- PDB-1tsd: THYMIDYLATE SYNTHASE COMPLEX WITH 2'-DEOXYURIDINE 5'-MONOPHOSPHAT... -

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Basic information

Entry
Database: PDB / ID: 1tsd
TitleTHYMIDYLATE SYNTHASE COMPLEX WITH 2'-DEOXYURIDINE 5'-MONOPHOSPHATE (DUMP) AND FOLATE ANALOG 1843U89
ComponentsTHYMIDYLATE SYNTHASE
KeywordsTRANSFERASE (METHYLTRANSFERASE) / DUMP / 1843U89
Function / homology
Function and homology information


thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / response to radiation / regulation of translation / methylation / magnesium ion binding / protein homodimerization activity / RNA binding ...thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / response to radiation / regulation of translation / methylation / magnesium ion binding / protein homodimerization activity / RNA binding / cytosol / cytoplasm
Similarity search - Function
Thymidylate Synthase; Chain A / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase, active site / Thymidylate synthase active site. / Thymidylate synthase / Thymidylate synthase/dCMP hydroxymethylase / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase superfamily / Thymidylate synthase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / Chem-F89 / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / Thymidylate synthase / Thymidylate synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 1.95 Å
AuthorsWeichsel, A. / Montfort, W.R.
Citation
Journal: Nat.Struct.Biol. / Year: 1995
Title: Ligand-induced distortion of an active site in thymidylate synthase upon binding anticancer drug 1843U89.
Authors: Weichsel, A. / Montfort, W.R.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1995
Title: Promotion of Purine Nucleotide Binding to Thymidylate Synthase by a Potent Folate Analogue Inhibitor, 1843U89
Authors: Weichsel, A. / Montfort, W.R. / Ciesla, J. / Maley, F.
#2: Journal: Biochemistry / Year: 1990
Title: Structure, Multiple Site Binding, and Segmental Accommodation in Thymidylate Synthase on Binding Dump and an Anti-Folate
Authors: Montfort, W.R. / Perry, K.M. / Fauman, E.B. / Finer-Moore, J.S. / Maley, G.F. / Hardy, L. / Maley, F. / Stroud, R.M.
History
DepositionAug 15, 1995Processing site: BNL
Revision 1.0Jan 29, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Other / Category: diffrn_detector / pdbx_database_status
Item: _diffrn_detector.detector / _pdbx_database_status.process_site
Revision 1.4Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: THYMIDYLATE SYNTHASE
B: THYMIDYLATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8618
Polymers61,0872
Non-polymers1,7746
Water3,387188
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8790 Å2
ΔGint-28 kcal/mol
Surface area19230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.520, 127.520, 68.250
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein THYMIDYLATE SYNTHASE


Mass: 30543.662 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
References: UniProt: P00470, UniProt: P0A884*PLUS, thymidylate synthase
#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#3: Chemical ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP


Mass: 308.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N2O8P
#4: Chemical ChemComp-F89 / S)-2-(5(((1,2-DIHYDRO-3-METHYL-1-OXOBENZO(F)QUINAZOLIN-9-YL)METHYL)AMINO)1-OXO-2-ISOINDOLINYL)GLUTARIC ACID / FOLATE ANALOG 1843U89


Mass: 500.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H24N4O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.07 %
Crystal
*PLUS
Density % sol: 52 %
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
131 mg/mlE. coli1drop
25 mMdUMP1drop
30.5 mM1843U891drop
420 mMphosphate1drop
520 mM2-mercaptoethanol1drop
62.6 Mammonium sulfate1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Jun 21, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→15 Å / Num. obs: 48550 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.087
Reflection
*PLUS
Rmerge(I) obs: 0.087

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Processing

Software
NameClassification
GPRLSArefinement
MADNESdata reduction
PROCORdata reduction
FBSCALEdata reduction
RefinementResolution: 1.95→7 Å / σ(F): 0 /
RfactorNum. reflection% reflection
obs0.197 41710 98.9 %
Displacement parametersBiso mean: 27 Å2
Refinement stepCycle: LAST / Resolution: 1.95→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4306 0 122 188 4616
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.020.02
X-RAY DIFFRACTIONp_angle_d0.0450.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0440.035
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.781.75
X-RAY DIFFRACTIONp_mcangle_it2.722.5
X-RAY DIFFRACTIONp_scbond_it4.7615
X-RAY DIFFRACTIONp_scangle_it4.732.5
X-RAY DIFFRACTIONp_plane_restr0.0180.02
X-RAY DIFFRACTIONp_chiral_restr0.2910.2
X-RAY DIFFRACTIONp_singtor_nbd0.210.3
X-RAY DIFFRACTIONp_multtor_nbd0.2210.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1960.3
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.85
X-RAY DIFFRACTIONp_staggered_tor2115
X-RAY DIFFRACTIONp_orthonormal_tor28.315
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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