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- PDB-8pts: human GUK1 in complex with compound AT8001 -

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Basic information

Entry
Database: PDB / ID: 8pts
Titlehuman GUK1 in complex with compound AT8001
ComponentsGuanylate kinase
KeywordsCONTRACTILE PROTEIN / complex intermediate compound inhibitor / kinase / Guanylate kinase
Function / homology
Function and homology information


dGDP biosynthetic process / dATP metabolic process / GDP biosynthetic process / GDP-mannose metabolic process / glycoprotein transport / guanylate kinase / dGMP metabolic process / purine nucleotide metabolic process / guanylate kinase activity / nucleobase-containing small molecule interconversion ...dGDP biosynthetic process / dATP metabolic process / GDP biosynthetic process / GDP-mannose metabolic process / glycoprotein transport / guanylate kinase / dGMP metabolic process / purine nucleotide metabolic process / guanylate kinase activity / nucleobase-containing small molecule interconversion / Interconversion of nucleotide di- and triphosphates / Azathioprine ADME / phosphorylation / xenobiotic metabolic process / photoreceptor inner segment / ATP binding / cytosol
Similarity search - Function
Guanylate kinase / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
: / Guanylate kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsZimberger, C. / Canard, B. / Ferron, F.
Funding support France, 1items
OrganizationGrant numberCountry
French Infrastructure for Integrated Structural Biology (FRISBI)ANR-10-INBS-0005 France
Citation
Journal: Plos Biol. / Year: 2024
Title: The activation cascade of the broad-spectrum antiviral bemnifosbuvir characterized at atomic resolution.
Authors: Chazot, A. / Zimberger, C. / Feracci, M. / Moussa, A. / Good, S. / Sommadossi, J.P. / Alvarez, K. / Ferron, F. / Canard, B.
#1: Journal: Biorxiv / Year: 2024
Title: The activation chain of the broad-spectrum antiviral bemnifosbuvir at atomic resolution
Authors: Chazot, A. / Zimberger, C. / Feracci, M. / Moussa, A. / Good, S. / Sommadossi, J.P. / Alvarez, K. / Ferron, F. / Canard, B.
History
DepositionJul 14, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2024Group: Database references / Category: citation / citation_author

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Guanylate kinase
B: Guanylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3585
Polymers43,5072
Non-polymers8513
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-1 kcal/mol
Surface area19460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.773, 54.273, 58.957
Angle α, β, γ (deg.)90.00, 108.79, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-315-

HOH

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Components

#1: Protein Guanylate kinase / GMP kinase / Guanylate kinase 1


Mass: 21753.584 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GUK1, GMK, GMPK
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q16774, guanylate kinase
#2: Chemical ChemComp-EIF / [(2~{R},3~{R},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-fluoranyl-4-methyl-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate


Mass: 379.238 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H15FN5O7P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O
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: 2.31 Å3/Da / Density % sol: 46.78 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 12 -17 % PEG330 66mM Na Cacodylate 33mM MES 66mM MgCl2
PH range: 6.5-7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.76→62.849 Å / Num. obs: 37848 / % possible obs: 96 % / Redundancy: 4.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.029 / Rrim(I) all: 0.063 / Net I/σ(I): 9.7
Reflection shellResolution: 1.763→1.793 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.699 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1925 / CC1/2: 0.825 / Rpim(I) all: 0.371 / Rrim(I) all: 0.796 / % possible all: 96.2

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (17-FEB-2023)refinement
autoPROCdata processing
Aimlessdata scaling
MoRDaphasing
autoPROCdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→62.849 Å / Cross valid method: THROUGHOUT
Details: HYDROGENS WERE FULLY REFINED WITH ZERO OCCUPANCY AT NUCLEAR POSITION.
RfactorNum. reflection% reflectionSelection details
Rfree0.26 --RANDOM
Rwork0.2481 ---
obs0.2497 37848 96 %-
Refinement stepCycle: LAST / Resolution: 1.76→62.849 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3019 0 56 119 3194
Refine LS restraints
Refine-IDType
X-RAY DIFFRACTIONo_bond_d
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it

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