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- PDB-9j8l: apo form of GMPK -

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Basic information

Entry
Database: PDB / ID: 9j8l
Titleapo form of GMPK
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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 21, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)43,9684
Polymers43,7832
Non-polymers1842
Water543
1
A: Guanylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9842
Polymers21,8921
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Guanylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9842
Polymers21,8921
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.728, 81.728, 219.227
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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


Mass: 21891.730 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 (E. coli) / References: UniProt: Q16774, guanylate kinase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.41 Å3/Da / Density % sol: 49.04 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 25% w/v PEG 3350, 0.2 M NaCl, 0.1 M Bis-Tris, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.9→43.85 Å / Num. obs: 10320 / % possible obs: 100 % / Redundancy: 12.2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.168 / Rpim(I) all: 0.05 / Rrim(I) all: 0.175 / Χ2: 0.99 / Net I/σ(I): 13.2 / Num. measured all: 126123
Reflection shellResolution: 2.9→3.08 Å / % possible obs: 100 % / Redundancy: 13.1 % / Rmerge(I) obs: 0.906 / Num. measured all: 21153 / Num. unique obs: 1610 / CC1/2: 0.9 / Rpim(I) all: 0.254 / Rrim(I) all: 0.942 / Χ2: 0.97 / 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: 6UNI

6uni


Resolution: 2.9→35.67 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2948 490 4.78 %
Rwork0.2445 --
obs0.2471 10260 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→35.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2853 0 12 3 2868
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042909
X-RAY DIFFRACTIONf_angle_d0.6363953
X-RAY DIFFRACTIONf_dihedral_angle_d4.814419
X-RAY DIFFRACTIONf_chiral_restr0.044463
X-RAY DIFFRACTIONf_plane_restr0.005525
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.190.40161010.3332369X-RAY DIFFRACTION100
3.19-3.650.32881090.2852402X-RAY DIFFRACTION100
3.65-4.60.30891370.2342416X-RAY DIFFRACTION100
4.6-35.670.24941430.20892583X-RAY DIFFRACTION100
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)
13.1538-0.92252.46171.13211.58276.6489-0.00710.23940.59480.03930.11660.2005-0.64960.1787-0.11070.5294-0.00360.16370.22990.14270.5237-18.0634-10.854619.1684
23.52953.41331.4328.53873.33787.96820.47650.0161-0.46421.28580.109-1.23760.6067-0.5253-0.56970.3942-0.0703-0.03510.43750.14340.5537-28.7505-16.947114.1862
34.5564-1.2749-0.29724.37830.52725.2490.29120.85690.085-0.0166-0.27940.18640.6449-1.17020.00320.48-0.1513-0.01730.40720.15820.4123-27.3216-20.31462.0713
46.78222.5592-3.59566.3137-1.70657.34380.1315-0.41780.6260.4938-0.5828-0.43160.17830.92420.41570.2771-0.065-0.03160.6217-0.00130.64274.4428-25.887327.4265
54.4035-0.91330.90049.032-4.22385.97550.4777-0.50290.64141.40430.57020.3024-2.1306-1.0976-0.65760.8815-0.08540.13021.732-0.16030.45775.9583-17.589319.0233
61.9928-7.0198-5.60456.87454.19626.04280.5179-0.61942.518-1.56091.19710.7932-0.6537-2.8786-1.5070.9480.1342-0.01651.44440.35241.0157-1.5004-5.63779.1923
74.5341-0.56532.43052.5979-1.63363.4879-0.5060.89510.312-0.06030.5514-0.09650.0603-1.2151-0.25540.6295-0.01220.04591.7476-0.10780.6256-7.0485-19.07416.5308
81.30070.917-2.75848.3944-6.59799.9608-0.17920.7735-0.2453-1.11830.24870.44571.0374-0.5357-0.09170.4927-0.0482-0.00690.6726-0.05920.36311.6558-27.670117.7008
97.8208-1.14711.35916.57431.98525.3075-0.303-0.2351-0.6424-0.12590.12580.38240.5971-0.18520.18260.4844-0.09630.0750.20470.03140.3267-12.3006-31.587236.3249
106.69630.2298-5.36753.5523-3.23326.5988-0.7393-1.2356-0.7332-0.1197-0.6408-0.62810.85362.44861.15960.59490.10530.15020.9430.22450.52688.5073-32.59528.8424
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 94 )
2X-RAY DIFFRACTION2chain 'A' and (resid 95 through 126 )
3X-RAY DIFFRACTION3chain 'A' and (resid 127 through 195 )
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 27 )
5X-RAY DIFFRACTION5chain 'B' and (resid 28 through 39 )
6X-RAY DIFFRACTION6chain 'B' and (resid 40 through 52 )
7X-RAY DIFFRACTION7chain 'B' and (resid 53 through 78 )
8X-RAY DIFFRACTION8chain 'B' and (resid 79 through 126 )
9X-RAY DIFFRACTION9chain 'B' and (resid 127 through 160 )
10X-RAY DIFFRACTION10chain 'B' and (resid 161 through 194 )

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