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- PDB-2xx3: HUMAN THYMIDYLATE KINASE COMPLEXED WITH thymidine butenyl phospho... -

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Basic information

Entry
Database: PDB / ID: 2xx3
TitleHUMAN THYMIDYLATE KINASE COMPLEXED WITH thymidine butenyl phosphonate monophosphate and ADP
ComponentsTHYMIDYLATE KINASE
KeywordsTRANSFERASE / ACYCLIC NUCLEOSIDE PHOSPHONATE
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 / 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
ADENOSINE-5'-DIPHOSPHATE / NITRATE ION / N1-[(E)-4-DIHYDROXYPHOSPHONYL-BUT-2-ENYL]-THYMINE / Thymidylate kinase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2 Å
AuthorsCaillat, C. / Meyer, P.
CitationJournal: J.Med.Chem. / Year: 2011
Title: Novel Antiviral C5-Substituted Pyrimidine Acyclic Nucleoside Phosphonates Selected as Human Thymidylate Kinase Substrates.
Authors: Topalis, D. / Pradere, U. / Roy, V. / Caillat, C. / Azzouzi, A. / Broggi, J. / Snoeck, R. / Andrei, G. / Lin, J. / Eriksson, S. / Alexandre, J.A.C. / El-Amri, C. / Deville-Bonne, D. / Meyer, ...Authors: Topalis, D. / Pradere, U. / Roy, V. / Caillat, C. / Azzouzi, A. / Broggi, J. / Snoeck, R. / Andrei, G. / Lin, J. / Eriksson, S. / Alexandre, J.A.C. / El-Amri, C. / Deville-Bonne, D. / Meyer, P. / Balzarini, J. / Agrofoglio, L.A.
History
DepositionNov 8, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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.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_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 KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8815
Polymers26,0281
Non-polymers8544
Water3,657203
1
A: THYMIDYLATE KINASE
hetero molecules

A: THYMIDYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,76310
Polymers52,0552
Non-polymers1,7078
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area3370 Å2
ΔGint-48.6 kcal/mol
Surface area17700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.440, 38.320, 73.160
Angle α, β, γ (deg.)90.00, 123.07, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2049-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein THYMIDYLATE KINASE / DTMP KINASE


Mass: 26027.740 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: 6 HISTIDINE TAG / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P23919, dTMP kinase

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Non-polymers , 5 types, 207 molecules

#2: 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
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-TAE / N1-[(E)-4-DIHYDROXYPHOSPHONYL-BUT-2-ENYL]-THYMINE


Mass: 340.164 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O8P2
#5: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 2.52 Å3/Da / Density % sol: 51.23 % / Description: NONE
Crystal growpH: 7.5 / Details: pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.2→35 Å / Num. obs: 16363 / % possible obs: 95.7 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Biso Wilson estimate: 19.74 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 7.9

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Processing

Software
NameVersionClassification
BUSTER2.8.0refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2→18.4 Å / Cor.coef. Fo:Fc: 0.9307 / Cor.coef. Fo:Fc free: 0.8841 / SU R Cruickshank DPI: 0.178 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.194 / SU Rfree Blow DPI: 0.169 / SU Rfree Cruickshank DPI: 0.163
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=ADP MG TAE NO3. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=1790. NUMBER WITH APPR DEFAULT CCP4 ATOM ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=ADP MG TAE NO3. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=1790. NUMBER WITH APPR DEFAULT CCP4 ATOM TYPE=52. NUMBER TREATED BY BAD NON-BONDED CONTACTS=1.
RfactorNum. reflection% reflectionSelection details
Rfree0.2354 1001 6.33 %RANDOM
Rwork0.1881 ---
obs0.1911 15820 --
Displacement parametersBiso mean: 26.88 Å2
Baniso -1Baniso -2Baniso -3
1--0.4355 Å20 Å21.9004 Å2
2---0.4645 Å20 Å2
3---0.9 Å2
Refine analyzeLuzzati coordinate error obs: 0.245 Å
Refinement stepCycle: LAST / Resolution: 2→18.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1585 0 53 203 1841
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0071667HARMONIC2
X-RAY DIFFRACTIONt_angle_deg12254HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d592SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes45HARMONIC2
X-RAY DIFFRACTIONt_gen_planes238HARMONIC5
X-RAY DIFFRACTIONt_it1646HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.24
X-RAY DIFFRACTIONt_other_torsion17.76
X-RAY DIFFRACTIONt_improper_torsion4HARMONIC0
X-RAY DIFFRACTIONt_chiral_improper_torsion202SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2094SEMIHARMONIC4
LS refinement shellResolution: 2→2.14 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2301 163 5.8 %
Rwork0.2166 2646 -
all0.2174 2809 -
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.6548-0.92990.41680.76160.79452.99620.04740.0297-0.06950.0051-0.0140.06910.09590.2003-0.0334-0.108-0.0075-0.00170.14290-0.1231-13.557610.2555.7779
20.84230.13810.15471.0966-0.3547-0.1557-0.01950.0035-0.0190.05550.01710.04970.05340.0230.0025-0.050.0376-0.03230.13470.0251-0.0607-18.82532.101721.2244
30.77210.06810.474400.17160.9607-0.0229-0.0118-0.01530.011-0.01690.05280.020.01680.0398-0.10630.005-0.0570.2271-0.0292-0.1405-26.62819.596328.1026
41.752-0.3683-0.51361.04240.40133.00030.0753-0.0873-0.15960.0667-0.0751-0.0320.00540.0804-0.0002-0.1025-0.016-0.00970.1839-0.0047-0.1627-16.572714.867519.1833
51.9423-0.7444-0.09750.0099-1.18410.99030.01860.0111-0.01940.04820.0380.10220.039-0.055-0.0566-0.11470.0065-0.01020.2443-0.0467-0.1284-33.955511.82597.663
60.65670.0263-0.22110.74220.15853.29650.05830.11820.22520.0443-0.0432-0.0748-0.29650.172-0.0151-0.1135-0.00230.01180.1575-0.0048-0.1402-17.339220.73587.1922
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 3-40)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 41-53)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 54-72)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 73-131)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 132-157)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 158-212)

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