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- PDB-7sql: Crystal structure of human uridine-cytidine kinase 2 complexed wi... -

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Basic information

Entry
Database: PDB / ID: 7sql
TitleCrystal structure of human uridine-cytidine kinase 2 complexed with a weak small molecule inhibitor
ComponentsUridine-cytidine kinase 2
KeywordsTransferase/Inhibitor / Kinase / Uridine kinase / Cytidine kinase / Inhibitor / transferase / Transferase-Inhibitor complex
Function / homology
Function and homology information


uridine/cytidine kinase / CTP salvage / ribosylnicotinamide kinase activity / uridine kinase activity / Pyrimidine salvage / cytidine kinase activity / UMP salvage / phosphorylation / ATP binding / identical protein binding ...uridine/cytidine kinase / CTP salvage / ribosylnicotinamide kinase activity / uridine kinase activity / Pyrimidine salvage / cytidine kinase activity / UMP salvage / phosphorylation / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Uridine kinase-like / Phosphoribulokinase/uridine kinase / Phosphoribulokinase / Uridine kinase family / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chem-AQX / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Uridine-cytidine kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsMashayekh, S. / Stunkard, L.M. / Kienle, M. / Mathews, I.I. / Khosla, C.
Funding support1items
OrganizationGrant numberCountry
Other privatePTA 1256351-1-GAMDE
CitationJournal: Biochemistry / Year: 2022
Title: Structure-Based Prototyping of Allosteric Inhibitors of Human Uridine/Cytidine Kinase 2 (UCK2).
Authors: Mashayekh, S. / Stunkard, L.M. / Kienle, M. / Mathews, I.I. / Khosla, C.
History
DepositionNov 5, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uridine-cytidine kinase 2
B: Uridine-cytidine kinase 2
C: Uridine-cytidine kinase 2
D: Uridine-cytidine kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,75917
Polymers112,4354
Non-polymers2,32413
Water4,197233
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Analyzed on a SEC column
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9350 Å2
ΔGint-4 kcal/mol
Surface area39270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.087, 93.893, 157.497
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Uridine-cytidine kinase 2 / UCK 2 / Cytidine monophosphokinase 2 / Testis-specific protein TSA903 / Uridine monophosphokinase 2


Mass: 28108.830 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UCK2, UMPK / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9BZX2, uridine/cytidine kinase

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Non-polymers , 6 types, 246 molecules

#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C6H14O4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C4H10O3
#6: Chemical ChemComp-AQX / N-(4-bromophenyl)-2-{[1-(4-fluorophenyl)-4-oxo-4,5-dihydro-1H-pyrazolo[3,4-d]pyrimidin-6-yl]sulfanyl}acetamide


Mass: 474.306 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H13BrFN5O2S / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.76 Å3/Da / Density % sol: 55.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 4% glycerol, 100 mM HEPES pH 6.9, 8% PEG 3350, and 30% PEG 400
Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K
Ambient temp details: liquid nitrogen stream at room temperature
Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 12, 2020
Details: Flat Si Rh coated M0, Kirkpatrick-Baez flat bent Si M1 & M2
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.4→39.7 Å / Num. obs: 49319 / % possible obs: 99.6 % / Redundancy: 11.9 % / CC1/2: 0.995 / Rmerge(I) obs: 0.233 / Rpim(I) all: 0.073 / Rrim(I) all: 0.245 / Net I/σ(I): 11.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.4-2.4811.23.0045046644990.4570.9723.1631.799.3
9.6-39.6711.40.04999308700.9990.0150.0513798.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation7.47 Å39.67 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UFQ

1ufq


Resolution: 2.4→39.7 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.916 / WRfactor Rfree: 0.238 / WRfactor Rwork: 0.1829 / FOM work R set: 0.8064 / SU B: 8.534 / SU ML: 0.194 / SU R Cruickshank DPI: 0.3172 / SU Rfree: 0.2488 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.317 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2566 2414 4.9 %RANDOM
Rwork0.1997 ---
obs0.2025 46673 98.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 138.21 Å2 / Biso mean: 48.388 Å2 / Biso min: 4.82 Å2
Baniso -1Baniso -2Baniso -3
1-1.07 Å2-0 Å20 Å2
2---1.25 Å20 Å2
3---0.18 Å2
Refinement stepCycle: final / Resolution: 2.4→39.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6788 0 236 234 7258
Biso mean--72.69 46.34 -
Num. residues----849
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0137215
X-RAY DIFFRACTIONr_bond_other_d0.0010.0156981
X-RAY DIFFRACTIONr_angle_refined_deg1.5031.6459743
X-RAY DIFFRACTIONr_angle_other_deg1.2151.58316055
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1515864
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.06222.828389
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.993151273
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3771547
X-RAY DIFFRACTIONr_chiral_restr0.0680.2926
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028053
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021671
LS refinement shellResolution: 2.4→2.462 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.338 166 -
Rwork0.274 3314 -
obs--96.4 %

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