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- PDB-9lo3: Transition state analogue(GMPK in complex with GMP, ADP, Mg2+ and... -

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Basic information

Entry
Database: PDB / ID: 9lo3
TitleTransition state analogue(GMPK in complex with GMP, ADP, Mg2+ and AlF4- at 277 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 / TRIETHYLENE GLYCOL / Guanylate kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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)23,1448
Polymers21,8921
Non-polymers1,2527
Water4,666259
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)96.292, 96.292, 44.901
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 , 7 types, 266 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-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-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
#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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 2.74 Å3/Da / Density % sol: 55.19 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 35% 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: 1.75→48.15 Å / Num. obs: 24185 / % possible obs: 100 % / Redundancy: 10.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.038 / Rrim(I) all: 0.126 / Χ2: 0.99 / Net I/σ(I): 18.4 / Num. measured all: 259480
Reflection shellResolution: 1.75→1.78 Å / % possible obs: 100 % / Redundancy: 11 % / Rmerge(I) obs: 0.803 / Num. measured all: 14596 / Num. unique obs: 1321 / CC1/2: 0.926 / Rpim(I) all: 0.253 / Rrim(I) all: 0.843 / Χ2: 0.75 / 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: 9JAI

9jai


Resolution: 1.75→30.55 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2011 1185 4.91 %
Rwork0.1633 --
obs0.1652 24150 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→30.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1507 0 79 259 1845
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071627
X-RAY DIFFRACTIONf_angle_d1.1232212
X-RAY DIFFRACTIONf_dihedral_angle_d18.473623
X-RAY DIFFRACTIONf_chiral_restr0.06248
X-RAY DIFFRACTIONf_plane_restr0.008283
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.830.27941360.20742848X-RAY DIFFRACTION100
1.83-1.930.24281390.18092870X-RAY DIFFRACTION100
1.93-2.050.22391600.1812843X-RAY DIFFRACTION100
2.05-2.20.1931450.1682833X-RAY DIFFRACTION100
2.21-2.430.20271500.17322872X-RAY DIFFRACTION100
2.43-2.780.23611500.16642870X-RAY DIFFRACTION100
2.78-3.50.18061500.16142879X-RAY DIFFRACTION100
3.5-30.550.17671550.14222950X-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)
14.2639-0.47810.15184.6684-0.30271.8016-0.0413-0.2454-0.20620.33460.0356-0.05710.0770.12750.03680.0646-0.02230.01770.2168-0.0190.1594-7.495-37.77862.5057
22.2585-0.1338-0.23951.38440.3212.2022-0.0452-0.0848-0.00150.0215-0.0155-0.0052-0.1840.0690.03880.07680.02890.00030.0672-0.00890.1107-19.5677-34.92063.867
32.88350.63090.64392.1334-0.05132.6161-0.06390.44970.2053-0.23230.02190.0247-0.3680.61420.02470.1631-0.03980.01780.22540.03210.1383-10.9843-29.8444-10.2755
42.8278-0.8479-0.2411.4588-0.41931.7363-0.0702-0.0211-0.08920.1009-0.0273-0.0649-0.15990.44590.00170.0222-0.07230.01750.4261-0.0280.1561.3814-35.37811.4351
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 27 )
2X-RAY DIFFRACTION2chain 'A' and (resid 28 through 112 )
3X-RAY DIFFRACTION3chain 'A' and (resid 113 through 160 )
4X-RAY DIFFRACTION4chain 'A' and (resid 161 through 194 )

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