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- PDB-9wd2: Thymidylate kinase of Helicobacter pylori -

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Basic information

Entry
Database: PDB / ID: 9wd2
TitleThymidylate kinase of Helicobacter pylori
ComponentsThymidylate kinase
KeywordsCYTOSOLIC PROTEIN / kinase / dTMP / dTDP / thymidine synthesis
Function / homology
Function and homology information


dTMP kinase / dUDP biosynthetic process / dTDP biosynthetic process / dTMP kinase activity / dTTP biosynthetic process / ATP binding / cytosol / cytoplasm
Similarity search - Function
Thymidylate kinase, conserved site / Thymidylate kinase signature. / Thymidylate kinase / Thymidylate kinase-like domain / Thymidylate kinase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / THYMIDINE-5'-PHOSPHATE / Thymidylate kinase
Similarity search - Component
Biological speciesHelicobacter pylori 26695 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKumari, K. / Gourinath, S.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India) India
CitationJournal: J.Struct.Biol. / Year: 2026
Title: Targeting Helicobacter pylori thymidylate kinase: structural insights and validation of novel inhibitors.
Authors: Kumari, K. / Khan, F.M. / Bose, M. / Ls, R.J. / Yadav, A. / Mondal, N. / Gourinath, S.
History
DepositionAug 18, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 12, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thymidylate kinase
B: Thymidylate kinase
C: Thymidylate kinase
D: Thymidylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,38516
Polymers86,9744
Non-polymers3,41112
Water1,71195
1
A: Thymidylate kinase
hetero molecules

D: Thymidylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1928
Polymers43,4872
Non-polymers1,7056
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_655y+1,x,-z1
Buried area4690 Å2
ΔGint-53 kcal/mol
Surface area15970 Å2
MethodPISA
2
B: Thymidylate kinase
hetero molecules

C: Thymidylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1928
Polymers43,4872
Non-polymers1,7056
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_655y+1,x,-z1
Buried area4670 Å2
ΔGint-45 kcal/mol
Surface area15830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.882, 93.882, 212.064
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
Thymidylate kinase / dTMP kinase


Mass: 21743.416 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori 26695 (bacteria) / Gene: tmk, HP_1474 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O26009, dTMP kinase
#2: Chemical
ChemComp-TMP / THYMIDINE-5'-PHOSPHATE


Mass: 322.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N2O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.7 Å3/Da / Density % sol: 54.52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 60% v/v Tacsimate pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.918 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Sep 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.449→48.5 Å / Num. obs: 35800 / % possible obs: 100 % / Redundancy: 25.1 % / CC1/2: 0.99 / Net I/σ(I): 1.1
Reflection shellResolution: 2.449→2.98 Å / Num. unique obs: 27210 / CC1/2: 0.83

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→48.44 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.902 / SU B: 31.01 / SU ML: 0.302 / Cross valid method: FREE R-VALUE / ESU R: 0.464 / ESU R Free: 0.309
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2802 2382 7.073 %
Rwork0.2148 31297 -
all0.22 --
obs-31297 99.964 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 58.007 Å2
Baniso -1Baniso -2Baniso -3
1--0.822 Å2-0 Å2-0 Å2
2---0.822 Å2-0 Å2
3---1.644 Å2
Refinement stepCycle: LAST / Resolution: 2.5→48.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5483 0 212 95 5790
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0125758
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165602
X-RAY DIFFRACTIONr_angle_refined_deg1.3821.6477789
X-RAY DIFFRACTIONr_angle_other_deg0.4671.5712873
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4625716
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.965523
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.13554
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.895101015
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.85510205
X-RAY DIFFRACTIONr_chiral_restr0.0690.2954
X-RAY DIFFRACTIONr_chiral_restr_other0.2090.24
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026339
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021145
X-RAY DIFFRACTIONr_nbd_refined0.2240.21253
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1920.25050
X-RAY DIFFRACTIONr_nbtor_refined0.1780.22812
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.23159
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2050.2166
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0890.23
X-RAY DIFFRACTIONr_metal_ion_refined0.2750.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3850.216
X-RAY DIFFRACTIONr_nbd_other0.1560.261
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.140.29
X-RAY DIFFRACTIONr_mcbond_it3.6924.1782906
X-RAY DIFFRACTIONr_mcbond_other3.6744.1782906
X-RAY DIFFRACTIONr_mcangle_it5.7587.4733608
X-RAY DIFFRACTIONr_mcangle_other5.7587.4753609
X-RAY DIFFRACTIONr_scbond_it4.1654.4392852
X-RAY DIFFRACTIONr_scbond_other4.1654.4392852
X-RAY DIFFRACTIONr_scangle_it6.478.0444181
X-RAY DIFFRACTIONr_scangle_other6.4698.0444182
X-RAY DIFFRACTIONr_lrange_it8.82840.9956363
X-RAY DIFFRACTIONr_lrange_other8.82841.0036356
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.5-2.5650.3681730.42222430.41824160.8740.8671000.426
2.565-2.6350.4111660.38822110.3923780.8840.90399.95790.389
2.635-2.7110.4061540.33421590.33923140.90.93499.95680.328
2.711-2.7940.3981520.29720990.30422520.8840.94799.95560.282
2.794-2.8860.3361350.27920490.28321840.9350.9521000.259
2.886-2.9860.3491770.24819200.25620970.9250.9591000.228
2.986-3.0990.2871570.23218980.23620550.9440.9671000.206
3.099-3.2250.3661340.23618550.24519890.9140.9661000.213
3.225-3.3670.2961240.22517730.2318970.9340.971000.202
3.367-3.5310.2541180.21316900.21518080.9560.9781000.195
3.531-3.7210.31310.21415980.2217290.9430.9781000.197
3.721-3.9450.2741270.1915280.19616550.9550.981000.173
3.945-4.2150.2081040.15214470.15515510.9760.9871000.138
4.215-4.550.2331080.15213590.15814670.9650.9861000.138
4.55-4.980.161860.14212650.14313510.9830.9871000.128
4.98-5.5610.29950.20611410.21312360.9570.9791000.191
5.561-6.4070.334830.24110100.24710930.9340.971000.219
6.407-7.8130.228610.2019060.2039670.9660.9781000.184
7.813-10.9080.196660.1486880.1527540.9780.9871000.145
10.908-48.4380.433310.3014580.314910.8150.91399.59270.282
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)
10.5042-0.0105-0.36390.35820.01120.91940.049-0.00680.02010.0269-0.0024-0.0136-0.0340.0221-0.04660.31930.01210.00450.3097-0.02010.004135.178717.4991-13.6704
21.44480.36570.20880.36740.31340.69940.09150.0235-0.10470.0265-0.0378-0.02710.0417-0.001-0.05370.3195-0.0451-0.03590.2784-0.01920.018247.6715-4.217812.1221
30.80150.7390.35940.78220.41130.55460.04420.0059-0.05030.0455-0.021-0.046-0.05690.0297-0.02320.3482-0.02970.01070.2861-0.01140.004119.6396-17.5842-7.969
41.10210.49980.2011.82040.1180.1820.04230.08570.00050.1247-0.0801-0.0776-0.16680.09750.03780.406-0.1623-0.05090.30160.02680.013732.2271-30.562732.7657
Refinement TLS groupSelection: ALL

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