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- PDB-1nn0: Crystal structure of human thymidylate kinase with ddTMP and ADP -

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Basic information

Entry
Database: PDB / ID: 1nn0
TitleCrystal structure of human thymidylate kinase with ddTMP and ADP
ComponentsThymidylate kinase
KeywordsTRANSFERASE / thymidylate kinase / p-loop / dideoxythymidine
Function / homology
Function and homology information


thymidine biosynthetic process / dTMP kinase / dUDP biosynthetic process / dTDP biosynthetic process / dTMP kinase activity / Interconversion of nucleotide di- and triphosphates / dTTP biosynthetic process / nucleoside diphosphate kinase activity / cellular response to growth factor stimulus / mitochondrion ...thymidine biosynthetic process / dTMP kinase / dUDP biosynthetic process / dTDP biosynthetic process / dTMP kinase activity / Interconversion of nucleotide di- and triphosphates / dTTP biosynthetic process / nucleoside diphosphate kinase activity / cellular response to growth factor stimulus / mitochondrion / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Thymidylate kinase, conserved site / Thymidylate kinase signature. / Thymidylate kinase / Thymidylate kinase-like domain / Thymidylate kinase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE / ADENOSINE-5'-DIPHOSPHATE / Thymidylate kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 Å
AuthorsOstermann, N. / Segura-Pena, D. / Meier, C. / Veit, T. / Monnerjahn, M. / Konrad, M. / Lavie, A.
CitationJournal: Biochemistry / Year: 2003
Title: Structures of human thymidylate kinase in complex with prodrugs: implications for the structure-based design of novel compounds
Authors: Ostermann, N. / Segura-Pena, D. / Meier, C. / Veit, T. / Monnerjahn, M. / Konrad, M. / Lavie, A.
History
DepositionJan 12, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thymidylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8355
Polymers24,0531
Non-polymers7824
Water5,495305
1
A: Thymidylate kinase
hetero molecules

A: Thymidylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,66910
Polymers48,1052
Non-polymers1,5648
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area4650 Å2
ΔGint-73 kcal/mol
Surface area17300 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)100.535, 100.535, 49.963
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Thymidylate kinase / dTMP kinase


Mass: 24052.533 Da / Num. of mol.: 1 / Mutation: R200A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DTYMK OR TYMK OR TMPK OR CDC8 / Production host: Escherichia coli (E. coli) / References: UniProt: P23919, dTMP kinase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-2DT / 3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE / 2',3'-DIDEOXYTHYMIDINE-5'-MONOPHOSPHATE


Type: DNA linking / Mass: 306.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N2O7P
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 15-20% PEG 3350, 100 mM Tris/HCl, pH 8.0, 5% filtered dead sea water, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12 mMprotein1drop
22 mMADP1drop

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID2 / Wavelength: 0.9887 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9887 Å / Relative weight: 1
ReflectionResolution: 1.55→70.7 Å / Num. obs: 35723 / % possible obs: 96.4 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 7.24
Reflection shellResolution: 1.55→1.6 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 1.32 / Rsym value: 0.364 / % possible all: 96.4
Reflection
*PLUS
% possible obs: 94.7 % / Num. measured all: 119378
Reflection shell
*PLUS
% possible obs: 96.4 % / Rmerge(I) obs: 0.364

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Processing

Software
NameClassification
MAR345data collection
XDSdata reduction
REFMACrefinement
XDSdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.6→50.3 Å / σ(F): 0
RfactorNum. reflection
Rfree0.265 3235
Rwork0.211 -
all-119378
obs-35723
Refinement stepCycle: LAST / Resolution: 1.6→50.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1641 0 49 305 1995
Refinement
*PLUS
Lowest resolution: 70.7 Å / Num. reflection obs: 32480 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.014
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg1.7

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