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- PDB-9lo6: Transition state analogue(GMPK in complex with GMP, ADP, Mg2+ and... -

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Basic information

Entry
Database: PDB / ID: 9lo6
TitleTransition state analogue(GMPK in complex with GMP, ADP, Mg2+ and AlF4- at 293 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 / ADENOSINE-5'-DIPHOSPHATE / TETRAFLUOROALUMINATE ION / Guanylate kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWang, L. / Ruan, K.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2024YFA1306201 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
DepositionJan 22, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Guanylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8095
Polymers21,8921
Non-polymers9184
Water3,171176
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)96.685, 96.685, 45.338
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 180 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: 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
#5: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 55.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 40% PEG4000, 0.1 M ammonium acetate, 0.1 M trisodium citrate, pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Oct 27, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 1.8→48.34 Å / Num. obs: 22625 / % possible obs: 99.9 % / Redundancy: 5.8 % / CC1/2: 1 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.017 / Rrim(I) all: 0.043 / Χ2: 1.05 / Net I/σ(I): 27.1 / Num. measured all: 131788
Reflection shellResolution: 1.8→1.84 Å / % possible obs: 100 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.259 / Num. measured all: 7831 / Num. unique obs: 1351 / CC1/2: 0.947 / Rpim(I) all: 0.117 / Rrim(I) all: 0.285 / Χ2: 0.96 / Net I/σ(I) obs: 6.8

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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: 9JAI

9jai


Resolution: 1.8→33.07 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2032 1133 5.01 %
Rwork0.1711 --
obs0.1727 22610 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→33.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1506 0 57 176 1739
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051589
X-RAY DIFFRACTIONf_angle_d0.9322160
X-RAY DIFFRACTIONf_dihedral_angle_d18.303599
X-RAY DIFFRACTIONf_chiral_restr0.052242
X-RAY DIFFRACTIONf_plane_restr0.008278
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.880.24841270.19182688X-RAY DIFFRACTION100
1.88-1.980.21311470.16262660X-RAY DIFFRACTION100
1.98-2.110.20751630.17862637X-RAY DIFFRACTION100
2.11-2.270.19481370.16712684X-RAY DIFFRACTION100
2.27-2.50.20781560.1892649X-RAY DIFFRACTION100
2.5-2.860.20931070.1852719X-RAY DIFFRACTION100
2.86-3.60.22081410.16782706X-RAY DIFFRACTION100
3.6-33.070.18211550.15892734X-RAY DIFFRACTION99
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)
12.0987-0.4163-0.68494.9526-0.46912.25570.0561-0.013-0.45130.1235-0.15010.30680.41980.29670.06120.16580.0396-0.00790.1203-0.00250.227-38.0971-11.634.4627
23.64850.86731.95085.09642.74266.38280.0171-0.04510.14910.0118-0.2380.2364-0.2536-0.15210.15320.0791-0.00410.00070.06860.00390.1324-46.16763.50270.3482
33.1372-0.60720.02483.69950.3343.2532-0.1018-0.04090.00220.1699-0.0279-0.2059-0.00110.39020.05730.0781-0.0149-0.01130.0999-0.0040.1284-35.7963-1.01196.6154
44.9673-1.1505-1.66984.6827-0.19743.95830.0636-0.25830.2701-0.0872-0.1764-0.26880.26540.70040.09140.14390.0880.00950.22410.04030.213-27.9072-9.14942.7543
55.1283-0.8086-0.67234.00081.464.85320.08420.20760.053-0.9088-0.3156-0.21040.78860.51610.17960.51870.10030.07850.44050.07070.1796-33.2999-4.0548-14.7607
61.95570.4461-1.08893.85780.16282.87920.1075-0.0584-0.1665-0.334-0.37170.01390.50080.58830.09880.28170.2341-0.04760.2095-0.01410.1863-29.789-18.84561.9339
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 39 )
2X-RAY DIFFRACTION2chain 'A' and (resid 40 through 66 )
3X-RAY DIFFRACTION3chain 'A' and (resid 67 through 112 )
4X-RAY DIFFRACTION4chain 'A' and (resid 113 through 126 )
5X-RAY DIFFRACTION5chain 'A' and (resid 127 through 160 )
6X-RAY DIFFRACTION6chain 'A' and (resid 161 through 194 )

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