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- PDB-9jab: Transition State Mimic(GMPK in complex with ADP, GMP , Mg2+, K+ a... -

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Basic information

Entry
Database: PDB / ID: 9jab
TitleTransition State Mimic(GMPK in complex with ADP, GMP , Mg2+, K+ and AlF4-)
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: 2.75 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)45,69712
Polymers43,7832
Non-polymers1,91410
Water1086
1
A: Guanylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8496
Polymers21,8921
Non-polymers9575
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Guanylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8496
Polymers21,8921
Non-polymers9575
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.632, 44.202, 66.695
Angle α, β, γ (deg.)72.73, 85.35, 78.76
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 6 types, 16 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#5: 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
#6: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: AlF4 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.12 Å3/Da / Density % sol: 41.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 35% 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: 0.98655 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 22, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98655 Å / Relative weight: 1
ReflectionResolution: 2.75→40.52 Å / Num. obs: 9129 / % possible obs: 97.8 % / Redundancy: 2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.052 / Rrim(I) all: 0.079 / Χ2: 0.57 / Net I/σ(I): 7.9 / Num. measured all: 18505
Reflection shellResolution: 2.75→2.9 Å / % possible obs: 97.3 % / Redundancy: 2 % / Rmerge(I) obs: 0.269 / Num. measured all: 2662 / Num. unique obs: 1310 / CC1/2: 0.904 / Rpim(I) all: 0.235 / Rrim(I) all: 0.359 / Χ2: 0.51 / Net I/σ(I) obs: 2

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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: 2.75→40.52 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 2.03 / Phase error: 32.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2774 484 5.31 %
Rwork0.2268 --
obs0.2296 9120 97.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.75→40.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2897 0 116 6 3019
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023061
X-RAY DIFFRACTIONf_angle_d0.6154173
X-RAY DIFFRACTIONf_dihedral_angle_d18.391125
X-RAY DIFFRACTIONf_chiral_restr0.037476
X-RAY DIFFRACTIONf_plane_restr0.004536
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-3.150.3461630.2752870X-RAY DIFFRACTION98
3.15-3.960.27391540.24192866X-RAY DIFFRACTION97
3.97-40.520.2561670.20092900X-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)
11.33250.2384-0.18812.3950.16341.7116-0.08480.31610.0393-0.37060.13120.0672-0.06980.2061-0.0340.4898-0.1264-0.0130.55040.00220.3023.73578.692315.1565
23.57231.54040.3762.99910.73053.23130.1748-0.40960.17080.2305-0.1760.2014-0.067-0.2119-0.01970.25150.0755-0.0090.3209-0.0160.2744-2.8531-8.765-15.4779
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 2 through 194)
2X-RAY DIFFRACTION2(chain 'B' and resid 3 through 194)

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