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- PDB-9jac: GMPK in complex with GMP -

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Basic information

Entry
Database: PDB / ID: 9jac
TitleGMPK in complex with GMP
ComponentsGuanylate kinase
KeywordsTRANSFERASE / guanylate kinase
Function / homology
Function and homology information


dATP metabolic process / dGDP biosynthetic process / GDP biosynthetic process / GDP-mannose metabolic process / guanylate kinase / purine nucleotide metabolic process / dGMP metabolic process / glycoprotein transport / GMP kinase activity / nucleobase-containing small molecule interconversion ...dATP metabolic process / dGDP biosynthetic process / GDP biosynthetic process / GDP-mannose metabolic process / guanylate kinase / purine nucleotide metabolic process / dGMP metabolic process / glycoprotein transport / GMP kinase activity / nucleobase-containing small molecule interconversion / Interconversion of nucleotide di- and triphosphates / Azathioprine ADME / photoreceptor inner segment / xenobiotic metabolic process / mitochondrion / 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
GUANOSINE-5'-MONOPHOSPHATE / Guanylate kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsWang, L. / Ruan, K.
Funding support China, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2019YFA0508400 China
National Natural Science Foundation of China (NSFC)22377119 China
Other privateYD9100002028 China
CitationJournal: Nat Commun / Year: 2025
Title: Comprehensive profiling of the catalytic conformations of human Guanylate kinase.
Authors: Wang, L. / Li, Z. / Xuan, Y. / Qin, J. / Li, S. / Zhong, F. / Song, Y. / Yang, K. / Lv, M. / Li, F. / Jiahai, Z. / Pan, Y. / Guang, S. / Zhao, Y. / Shi, Y. / Liu, X. / Du, Y. / Gao, J. / Ruan, K.
History
DepositionAug 24, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Guanylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3473
Polymers21,8921
Non-polymers4552
Water5,098283
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.362, 96.362, 45.566
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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


Mass: 21891.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GUK1, GMK, GMPK / Production host: Escherichia coli (E. coli) / References: UniProt: Q16774, guanylate kinase
#2: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O8P / 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.: 283 / 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: 2.79 Å3/Da / Density % sol: 55.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 35% PEG4000, 0.1 M Ammonium acetate, 0.1 M Trisodium citrate, pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 20, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.47→48.18 Å / Num. obs: 40564 / % possible obs: 98.3 % / Redundancy: 9.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.016 / Rrim(I) all: 0.049 / Χ2: 1.08 / Net I/σ(I): 26.7 / Num. measured all: 371908
Reflection shellResolution: 1.47→1.5 Å / % possible obs: 98 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.503 / Num. measured all: 9157 / Num. unique obs: 1965 / CC1/2: 0.798 / Rpim(I) all: 0.259 / Rrim(I) all: 0.571 / Χ2: 1.36 / Net I/σ(I) obs: 3.6

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Processing

Software
NameVersionClassification
PHENIX(1.19_4092: ???)refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LVG

1lvg


Resolution: 1.47→30.77 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2006 2049 5.08 %
Rwork0.1639 --
obs0.1658 40314 97.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.47→30.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1480 0 30 283 1793
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071553
X-RAY DIFFRACTIONf_angle_d0.9292112
X-RAY DIFFRACTIONf_dihedral_angle_d14.204584
X-RAY DIFFRACTIONf_chiral_restr0.077243
X-RAY DIFFRACTIONf_plane_restr0.007275
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.47-1.50.36521380.29212529X-RAY DIFFRACTION97
1.5-1.540.341240.31782374X-RAY DIFFRACTION92
1.54-1.580.20061380.15972533X-RAY DIFFRACTION98
1.58-1.630.18211170.14912529X-RAY DIFFRACTION97
1.63-1.680.24891300.16352560X-RAY DIFFRACTION98
1.68-1.740.21021470.16092540X-RAY DIFFRACTION98
1.74-1.810.19631430.1522555X-RAY DIFFRACTION99
1.81-1.90.20921410.14922548X-RAY DIFFRACTION98
1.9-20.22541140.16762534X-RAY DIFFRACTION97
2-2.120.20851270.17382564X-RAY DIFFRACTION98
2.12-2.280.20271150.14752597X-RAY DIFFRACTION98
2.28-2.510.2051600.16522574X-RAY DIFFRACTION99
2.51-2.880.19361610.17192594X-RAY DIFFRACTION99
2.88-3.620.22231400.15922575X-RAY DIFFRACTION98
3.63-30.770.15371540.14992659X-RAY DIFFRACTION99

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