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- PDB-1nmz: Crystal structure of human thymidylate kinase with NH2TMP and AppNHp -

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Basic information

Entry
Database: PDB / ID: 1nmz
TitleCrystal structure of human thymidylate kinase with NH2TMP and AppNHp
Componentssimilar to THYMIDYLATE KINASE (DTMP KINASE)
KeywordsTRANSFERASE / thymidylate kinase / p-loop / aminothymidine
Function / homology
Function and homology information


thymidine biosynthetic process / dUDP biosynthetic process / dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / Interconversion of nucleotide di- and triphosphates / myoblast differentiation / nucleoside diphosphate kinase activity / dTTP biosynthetic process / response to cadmium ion ...thymidine biosynthetic process / dUDP biosynthetic process / dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / Interconversion of nucleotide di- and triphosphates / myoblast differentiation / nucleoside diphosphate kinase activity / dTTP biosynthetic process / response to cadmium ion / cellular response to growth factor stimulus / response to estrogen / mitochondrial matrix / mitochondrion / ATP binding / nucleus / cytosol / cytoplasm
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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / 3'-DEOXY-3'-AMINOTHYMIDINE MONOPHOSPHATE / Thymidylate kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.75 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

Downloads & links

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Assembly

Deposited unit
A: similar to THYMIDYLATE KINASE (DTMP KINASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9295
Polymers24,0531
Non-polymers8764
Water5,080282
1
A: similar to THYMIDYLATE KINASE (DTMP KINASE)
hetero molecules

A: similar to THYMIDYLATE KINASE (DTMP KINASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,85710
Polymers48,1052
Non-polymers1,7528
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area4760 Å2
ΔGint-41 kcal/mol
Surface area17110 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)101.301, 101.301, 49.513
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-402-

MG

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Components

#1: Protein similar to 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) / 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-NYM / 3'-DEOXY-3'-AMINOTHYMIDINE MONOPHOSPHATE / PHOSPHORIC ACID MONO-[3-AMINO-5-(5-METHYL-2,4-DIOXO-3,4-DIHYDRO-2H-PYRIMIDIN-1-YL)-TETRAHYDRO-FURAN-2-YLMETHYL] ESTER


Type: DNA linking / Mass: 321.224 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N3O7P
#4: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.29 Å3/Da / Density % sol: 45.87 %
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 mMAppNHp1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→71.6 Å / Num. obs: 25995 / % possible obs: 97.1 %
Reflection shellResolution: 1.75→1.8 Å / Rsym value: 0.352 / % possible all: 97.2
Reflection
*PLUS
Num. measured all: 142253 / Rmerge(I) obs: 0.045
Reflection shell
*PLUS
% possible obs: 97.2 % / Rmerge(I) obs: 0.352

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Processing

Software
NameClassification
MAR345data collection
XDSdata reduction
REFMACrefinement
XDSdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.75→71.6 Å / σ(F): 0
RfactorNum. reflection
Rfree0.243 2615
Rwork0.186 -
all-142253
obs-25995
Refinement stepCycle: LAST / Resolution: 1.75→71.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1641 0 54 282 1977
Refinement
*PLUS
Num. reflection obs: 25828 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.012
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg1.8

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