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- PDB-6zje: Crystal structure of human adenylate kinase 3, AK3, in complex wi... -

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Basic information

Entry
Database: PDB / ID: 6zje
TitleCrystal structure of human adenylate kinase 3, AK3, in complex with inhibitor Ap5A
ComponentsGTP:AMP phosphotransferase AK3, mitochondrial
KeywordsTRANSFERASE / GTP:AMP PHOSPHOTRANSFERASE / Ap5A
Function / homology
Function and homology information


UTP metabolic process / ITP metabolic process / nucleoside-triphosphate-adenylate kinase / nucleoside triphosphate adenylate kinase activity / AMP metabolic process / ADP biosynthetic process / nucleoside triphosphate biosynthetic process / GTP metabolic process / blood coagulation / Factors involved in megakaryocyte development and platelet production ...UTP metabolic process / ITP metabolic process / nucleoside-triphosphate-adenylate kinase / nucleoside triphosphate adenylate kinase activity / AMP metabolic process / ADP biosynthetic process / nucleoside triphosphate biosynthetic process / GTP metabolic process / blood coagulation / Factors involved in megakaryocyte development and platelet production / mitochondrial matrix / phosphorylation / GTP binding / mitochondrion / ATP binding / cytoplasm
Similarity search - Function
Adenylate kinase 3/4, mitochondrial / Adenylate kinase, active site lid domain superfamily / Adenylate kinase, active site lid domain / Adenylate kinase, active site lid / Adenylate kinase subfamily / Adenylate kinase / Adenylate kinase, conserved site / Adenylate kinase signature. / Adenylate kinase/UMP-CMP kinase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
BIS(ADENOSINE)-5'-PENTAPHOSPHATE / GTP:AMP phosphotransferase AK3, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsGrundstrom, C. / Rogne, P. / Wolf-Watz, M. / Sauer-Eriksson, A.E.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council Sweden
CitationJournal: Biochemistry / Year: 2020
Title: Structural Basis for GTP versus ATP Selectivity in the NMP Kinase AK3.
Authors: Rogne, P. / Dulko-Smith, B. / Goodman, J. / Rosselin, M. / Grundstrom, C. / Hedberg, C. / Nam, K. / Sauer-Eriksson, A.E. / Wolf-Watz, M.
History
DepositionJun 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GTP:AMP phosphotransferase AK3, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6346
Polymers25,5991
Non-polymers1,0355
Water5,549308
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-37 kcal/mol
Surface area11910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.716, 62.639, 50.162
Angle α, β, γ (deg.)90.000, 108.010, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein GTP:AMP phosphotransferase AK3, mitochondrial / Adenylate kinase 3 / AK 3 / Adenylate kinase 3 alpha-like 1


Mass: 25599.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AK3, AK3L1, AK6, AKL3L / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UIJ7, nucleoside-triphosphate-adenylate kinase

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Non-polymers , 5 types, 313 molecules

#2: Chemical ChemComp-AP5 / BIS(ADENOSINE)-5'-PENTAPHOSPHATE


Mass: 916.367 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H29N10O22P5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 308 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.49 Å3/Da / Density % sol: 50.66 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Purified hAK3 was dialyzed against 30 mM MOPS buffer with 50 mM NaCl pH 7.0 and concentrated to 15-20 mg per ml. The resevoir contained 0.2 M CaCl2, 0.1 M Tris pH 8.0 and 20% PEG 6000. Drop ...Details: Purified hAK3 was dialyzed against 30 mM MOPS buffer with 50 mM NaCl pH 7.0 and concentrated to 15-20 mg per ml. The resevoir contained 0.2 M CaCl2, 0.1 M Tris pH 8.0 and 20% PEG 6000. Drop size 1 plus 1 microliter. Cryo protection 30% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.48→42.72 Å / Num. obs: 39892 / % possible obs: 95.1 % / Redundancy: 6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.033 / Net I/σ(I): 14.9
Reflection shellResolution: 1.48→1.53 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.852 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3174 / CC1/2: 0.521 / Rpim(I) all: 0.707 / % possible all: 76.1

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1zd8

1zd8


Resolution: 1.48→40.624 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 19.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1836 1995 5 %
Rwork0.1433 37897 -
obs0.1453 39892 95.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.64 Å2 / Biso mean: 30.4604 Å2 / Biso min: 15.27 Å2
Refinement stepCycle: final / Resolution: 1.48→40.624 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1719 0 118 314 2151
Biso mean--65.14 42.11 -
Num. residues----214
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.48-1.5170.30371120.2065213175
1.517-1.5580.23611180.1978223780
1.558-1.60390.21861290.1773243785
1.6039-1.65570.22661360.1605259192
1.6557-1.71480.24181480.16062826100
1.7148-1.78350.22321510.14212854100
1.7835-1.86470.17851480.13772819100
1.8647-1.9630.19531500.13272840100
1.963-2.0860.17941490.13552837100
2.086-2.2470.19971510.12982856100
2.247-2.47310.17941480.13142833100
2.4731-2.83090.17441510.14072862100
2.8309-3.56630.19081510.14032876100
3.5663-40.6240.16031530.14922898100

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