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

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Basic information

Entry
Database: PDB / ID: 6zjb
TitleCrystal structure of human adenylate kinase 3, AK3, in complex with inhibitor Gp5A
ComponentsGTP:AMP phosphotransferase AK3, mitochondrial
KeywordsTRANSFERASE / GTP:AMP PHOSPHOTRANSFERASE / Gp5A
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
P1-(5'-ADENOSYL)-P5-(5'-GUANOSYL) PENTAPHOSPHATE / GTP:AMP phosphotransferase AK3, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.822 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
B: GTP:AMP phosphotransferase AK3, mitochondrial
C: GTP:AMP phosphotransferase AK3, mitochondrial
D: GTP:AMP phosphotransferase AK3, mitochondrial
E: GTP:AMP phosphotransferase AK3, mitochondrial
F: GTP:AMP phosphotransferase AK3, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,33618
Polymers153,5966
Non-polymers5,74012
Water13,926773
1
A: GTP:AMP phosphotransferase AK3, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5563
Polymers25,5991
Non-polymers9572
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GTP:AMP phosphotransferase AK3, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5563
Polymers25,5991
Non-polymers9572
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: GTP:AMP phosphotransferase AK3, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5563
Polymers25,5991
Non-polymers9572
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: GTP:AMP phosphotransferase AK3, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5563
Polymers25,5991
Non-polymers9572
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: GTP:AMP phosphotransferase AK3, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5563
Polymers25,5991
Non-polymers9572
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: GTP:AMP phosphotransferase AK3, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5563
Polymers25,5991
Non-polymers9572
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.468, 66.760, 105.909
Angle α, β, γ (deg.)93.790, 93.950, 89.710
Int Tables number1
Space group name H-MP1

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Components

#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.: 6
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
#2: Chemical
ChemComp-G5P / P1-(5'-ADENOSYL)-P5-(5'-GUANOSYL) PENTAPHOSPHATE


Mass: 932.366 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C20H29N10O23P5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 773 / Source method: isolated from a natural source / Formula: H2O
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: 2.08 Å3/Da / Density % sol: 40.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
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 20% isopropanol, 0.1 M NaCitrate pH 5.6 and 20% PEG ...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 20% isopropanol, 0.1 M NaCitrate pH 5.6 and 20% PEG 4000. Drop size 1 plus 1 microliter.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.822→45.36 Å / Num. obs: 103037 / % possible obs: 93.1 % / Redundancy: 1.9 % / CC1/2: 0.995 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.093 / Net I/σ(I): 7.3
Reflection shellResolution: 1.822→1.95 Å / Rmerge(I) obs: 0.644 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 9068 / CC1/2: 0.632 / Rpim(I) all: 0.6 / % possible all: 80.9

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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: 1.822→45.36 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 29.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2565 5307 5.15 %
Rwork0.1916 97690 -
obs0.195 102997 92.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 134.22 Å2 / Biso mean: 37.9739 Å2 / Biso min: 13.13 Å2
Refinement stepCycle: final / Resolution: 1.822→45.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10403 0 354 798 11555
Biso mean--29.73 36.52 -
Num. residues----1300
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8221-1.84280.4704970.3811211761
1.8428-1.86450.43381850.3629322093
1.8645-1.88720.38661720.33327292
1.8872-1.91110.31871760.3119324993
1.9111-1.93620.36861810.2817321093
1.9362-1.96280.35671670.2691336294
1.9628-1.99080.31611680.264327194
1.9908-2.02050.30741920.2514328394
2.0205-2.05210.30331740.2404327094
2.0521-2.08570.30591720.2314328993
2.0857-2.12170.2941890.2316324594
2.1217-2.16030.31831690.2352340695
2.1603-2.20180.28371580.2224322893
2.2018-2.24680.29021580.2198329793
2.2468-2.29560.26981740.202329094
2.2956-2.3490.28591800.1972324794
2.349-2.40780.29391830.1934333194
2.4078-2.47290.26771900.1893325194
2.4729-2.54560.24912090.1894326994
2.5456-2.62780.27031940.1826332395
2.6278-2.72170.28231750.1863333696
2.7217-2.83070.24211890.1884333995
2.8307-2.95950.28091950.2008328295
2.9595-3.11550.25452090.1935336095
3.1155-3.31060.25031960.1784330595
3.3106-3.56610.23561880.1728328995
3.5661-3.92480.2121770.162332094
3.9248-4.49230.23351380.1499334094
4.4923-5.65810.2121690.1539332395
5.6581-45.360.20851830.1842336696

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