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- PDB-9jai: GMPK in complex with GMP and ADP -

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Basic information

Entry
Database: PDB / ID: 9jai
TitleGMPK in complex with GMP and ADP
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 / ADENOSINE-5'-DIPHOSPHATE / Guanylate kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)45,3646
Polymers43,7832
Non-polymers1,5814
Water1,63991
1
A: Guanylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6823
Polymers21,8921
Non-polymers7902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Guanylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6823
Polymers21,8921
Non-polymers7902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.770, 62.920, 66.160
Angle α, β, γ (deg.)90.00, 107.31, 90.00
Int Tables number4
Space group name H-MP1211

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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-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 1.99 Å3/Da / Density % sol: 38.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 40% PEG4000, 0.1 M ammonium acetate, 0.1 M trisodium citrate, pH 5.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97851 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97851 Å / Relative weight: 1
ReflectionResolution: 2.3→44.58 Å / Num. obs: 15194 / % possible obs: 99.1 % / Redundancy: 3.9 % / CC1/2: 0.977 / Rmerge(I) obs: 0.208 / Rpim(I) all: 0.12 / Rrim(I) all: 0.24 / Χ2: 0.98 / Net I/σ(I): 5.4 / Num. measured all: 59586
Reflection shellResolution: 2.3→2.39 Å / % possible obs: 99 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.637 / Num. measured all: 6137 / Num. unique obs: 1570 / CC1/2: 0.755 / Rpim(I) all: 0.368 / Rrim(I) all: 0.738 / Χ2: 0.92 / Net I/σ(I) obs: 2.3

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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: 2.3→31.58 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2489 838 5.52 %
Rwork0.1949 --
obs0.1978 15169 98.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→31.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2896 0 102 91 3089
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033051
X-RAY DIFFRACTIONf_angle_d0.6774151
X-RAY DIFFRACTIONf_dihedral_angle_d10.31451
X-RAY DIFFRACTIONf_chiral_restr0.04474
X-RAY DIFFRACTIONf_plane_restr0.003531
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.440.27161400.21762351X-RAY DIFFRACTION99
2.44-2.630.29991430.22282384X-RAY DIFFRACTION99
2.63-2.90.24831340.21632378X-RAY DIFFRACTION99
2.9-3.320.29361600.20362382X-RAY DIFFRACTION99
3.32-4.180.21841280.17172405X-RAY DIFFRACTION99
4.18-31.580.21071330.18122431X-RAY DIFFRACTION98
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)
12.6017-0.4703-0.20731.3478-0.05671.21860.01850.2034-0.4373-0.1581-0.05990.27840.0814-0.34670.01280.12630.0186-0.04070.2036-0.03280.125610.85039.333614.5873
20.4612-1.3563-0.2314.45-0.48084.99090.0785-0.43880.1337-0.28550.0987-0.4408-0.13650.2296-0.05050.0789-0.0649-0.03610.25750.04590.194625.338118.44913.763
38.1496-2.68016.4113.9815-2.6229.4314-0.29020.17510.3828-0.07890.0586-0.1604-0.6493-0.41060.18490.16160.00440.05220.18840.00080.017913.915518.588810.0085
41.71160.1133-0.43252.952-0.63931.44030.1526-0.0109-0.11840.1949-0.1598-0.00260.08240.1310.00510.0977-0.0052-0.03250.2134-0.01010.079313.802611.335424.8245
53.1139-1.53190.55682.4271-1.90471.8312-0.3156-0.25620.07651.00290.201-0.5644-0.2420.47250.1190.24110.0086-0.05940.2752-0.05690.19638.751414.546332.2712
61.3134-0.59341.16824.388-0.41455.0741-0.2354-0.145-0.1388-0.3092-0.01020.6171-0.5455-0.66120.17670.1248-0.0806-0.0720.33540.02650.3218-5.04213.949719.8914
70.70020.33190.67733.40151.74971.3619-0.3318-0.2887-0.01960.73980.4518-0.52140.0940.222-0.09110.1495-0.0024-0.06140.2918-0.1140.227117.52188.0329-9.9973
82.35570.26810.20354.74511.11075.442-0.11720.2593-0.2040.24260.03260.71870.285-1.13770.08380.15680.0053-0.00560.3717-0.04670.25053.127316.5688-5.944
91.1731-0.3713-0.23561.86232.20573.5805-0.124-0.27480.0309-0.05830.2319-0.1327-0.0358-0.1035-0.08440.16480.02860.01060.2466-0.01040.094816.038417.3164-11.6699
104.5647-0.1705-3.61492.62221.3079.2178-0.3280.3715-0.50240.0648-0.00740.32580.81140.04870.0490.2128-0.0031-0.11290.203-0.04210.1633.90330.6192-21.7024
113.9746-0.5433-1.21060.2506-0.13790.90530.1451-0.20810.1263-0.1759-0.05490.0178-0.25240.1029-0.08630.2469-0.0452-0.01080.1819-0.06260.151511.132410.9101-24.745
123.55442.55332.45623.2767-0.5156.63020.0685-0.60970.37320.0062-0.1005-0.8124-0.39440.51780.03350.1248-0.0006-0.05010.2749-0.09370.465627.20294.6487-15.3466
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 57 )
2X-RAY DIFFRACTION2chain 'A' and (resid 58 through 78 )
3X-RAY DIFFRACTION3chain 'A' and (resid 79 through 94 )
4X-RAY DIFFRACTION4chain 'A' and (resid 95 through 150 )
5X-RAY DIFFRACTION5chain 'A' and (resid 151 through 173 )
6X-RAY DIFFRACTION6chain 'A' and (resid 174 through 194 )
7X-RAY DIFFRACTION7chain 'B' and (resid 5 through 39 )
8X-RAY DIFFRACTION8chain 'B' and (resid 40 through 78 )
9X-RAY DIFFRACTION9chain 'B' and (resid 79 through 126 )
10X-RAY DIFFRACTION10chain 'B' and (resid 127 through 141 )
11X-RAY DIFFRACTION11chain 'B' and (resid 142 through 173 )
12X-RAY DIFFRACTION12chain 'B' and (resid 174 through 191 )

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