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- PDB-9jad: GMPK in complex with GMP and K+ -

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Basic information

Entry
Database: PDB / ID: 9jad
TitleGMPK in complex with GMP and K+
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 / ACETATE ION / : / Guanylate kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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)22,3534
Polymers21,8921
Non-polymers4613
Water4,143230
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)96.252, 96.252, 45.427
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-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.77 Å3/Da / Density % sol: 55.67 %
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: 1.55→48.13 Å / Num. obs: 35047 / % possible obs: 100 % / Redundancy: 9.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.022 / Rrim(I) all: 0.077 / Χ2: 0.85 / Net I/σ(I): 20.8 / Num. measured all: 333690
Reflection shellResolution: 1.55→1.58 Å / % possible obs: 99.6 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.395 / Num. measured all: 8222 / Num. unique obs: 1716 / CC1/2: 0.851 / Rpim(I) all: 0.196 / Rrim(I) all: 0.443 / Χ2: 0.83 / Net I/σ(I) obs: 3.4

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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: 1.55→31.51 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2039 1565 4.58 %
Rwork0.1655 --
obs0.1673 34157 97.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→31.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1469 0 29 230 1728
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081538
X-RAY DIFFRACTIONf_angle_d1.0042089
X-RAY DIFFRACTIONf_dihedral_angle_d7.8223
X-RAY DIFFRACTIONf_chiral_restr0.059239
X-RAY DIFFRACTIONf_plane_restr0.008274
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.60.31061480.21912711X-RAY DIFFRACTION91
1.6-1.660.22911300.19332837X-RAY DIFFRACTION93
1.66-1.720.22741200.18692900X-RAY DIFFRACTION96
1.72-1.80.24811540.18182919X-RAY DIFFRACTION97
1.8-1.90.22291640.16252941X-RAY DIFFRACTION98
1.9-2.020.19991300.15223001X-RAY DIFFRACTION99
2.02-2.170.2021590.15073005X-RAY DIFFRACTION100
2.17-2.390.20341430.16373020X-RAY DIFFRACTION100
2.39-2.740.23571350.17483061X-RAY DIFFRACTION100
2.74-3.440.19381430.17213060X-RAY DIFFRACTION100
3.45-31.510.1791390.15553137X-RAY DIFFRACTION100

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