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- PDB-7ueo: PANK3 complex structure with compound PZ-3977 -

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Basic information

Entry
Database: PDB / ID: 7ueo
TitlePANK3 complex structure with compound PZ-3977
ComponentsPantothenate kinase 3
KeywordsTRANSFERASE / PANK / Substrate / Complex / Pantothenate kinase / Inhibitor / Activator
Function / homology
Function and homology information


Coenzyme A biosynthesis / acetyl-CoA binding / vitamin binding / pantothenate kinase / pantothenate kinase activity / coenzyme A biosynthetic process / phosphorylation / protein homodimerization activity / ATP binding / nucleus / cytosol
Similarity search - Function
Fumble / Type II pantothenate kinase / ATPase, nucleotide binding domain
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Chem-Y90 / Pantothenate kinase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWhite, S.W. / Yun, M. / Lee, R.E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2024
Title: Development of Brain Penetrant Pyridazine Pantothenate Kinase Activators.
Authors: Tangallapally, R. / Subramanian, C. / Yun, M.K. / Edwards, A. / Sharma, L.K. / Yang, L. / Creed, K. / Wang, J. / Jackowski, S. / Rock, C.O. / White, S.W. / Lee, R.E.
History
DepositionMar 22, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 2.0Apr 12, 2023Group: Atomic model / Category: atom_site / Item: _atom_site.occupancy
Revision 2.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.2Oct 9, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pantothenate kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1466
Polymers42,1261
Non-polymers1,0205
Water2,882160
1
A: Pantothenate kinase 3
hetero molecules

A: Pantothenate kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,29212
Polymers84,2522
Non-polymers2,04010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area9150 Å2
ΔGint-43 kcal/mol
Surface area27350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.904, 97.904, 69.099
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-660-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Pantothenate kinase 3 / hPanK3 / Pantothenic acid kinase 3


Mass: 42125.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PANK3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H999, pantothenate kinase

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Non-polymers , 5 types, 165 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-Y90 / 6-{4-[(4-cyclopropyl-2-fluorophenyl)acetyl]piperazin-1-yl}pyridazine-3-carbonitrile


Mass: 365.404 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H20FN5O / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 2.27 Å3/Da / Density % sol: 45.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: PEG 4000, ammonium acetate, citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 35644 / % possible obs: 99.9 % / Redundancy: 11.2 % / Biso Wilson estimate: 23.17 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.076 / Net I/σ(I): 37.3
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.905 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 2195 / CC1/2: 0.857 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6B3V

6b3v


Resolution: 1.8→42.39 Å / SU ML: 0.1878 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.2404 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1971 1778 4.99 %
Rwork0.173 33845 -
obs0.1742 35623 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.13 Å2
Refinement stepCycle: LAST / Resolution: 1.8→42.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2712 0 67 160 2939
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00962845
X-RAY DIFFRACTIONf_angle_d1.15313853
X-RAY DIFFRACTIONf_chiral_restr0.0734428
X-RAY DIFFRACTIONf_plane_restr0.0064485
X-RAY DIFFRACTIONf_dihedral_angle_d15.96191663
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.23021290.20772573X-RAY DIFFRACTION99.01
1.85-1.90.23061370.19652573X-RAY DIFFRACTION99.63
1.9-1.970.22921370.19062558X-RAY DIFFRACTION99.7
1.97-2.040.23771360.17462597X-RAY DIFFRACTION99.74
2.04-2.120.26331350.17572545X-RAY DIFFRACTION99.89
2.12-2.210.19671360.17592595X-RAY DIFFRACTION99.93
2.21-2.330.23171350.17392583X-RAY DIFFRACTION100
2.33-2.480.20871350.17382589X-RAY DIFFRACTION100
2.48-2.670.19261400.16982625X-RAY DIFFRACTION100
2.67-2.940.19691350.17152584X-RAY DIFFRACTION100
2.94-3.360.16781380.1692631X-RAY DIFFRACTION100
3.36-4.230.17041420.15762647X-RAY DIFFRACTION100
4.23-42.390.19341430.17842745X-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)
11.610705237450.239610490767-0.7646934795190.88680438683-0.1537292795611.491281144020.0794673445586-0.27903521578-0.009558803616540.144660416883-0.1148702429630.0794628067421-0.05696415986990.1114315644590.02652714096630.155787845513-0.0306936195574-0.007288304078740.1484692497710.0004521305843880.132195915681-21.85622.068-6.201
25.40867103760.3489780544860.3293543605865.424804137892.101755110915.122284807750.01557078191640.0471930601267-0.121808343861-0.1751735481170.1404040470610.0930910419260.0408343260199-0.0707634728719-0.1468201416180.1789769737310.009152954861450.01471995669830.1831375118980.01778970232850.184984962882-21.80116.041-9.759
34.464191143745.56805675866-5.015649284588.97567419184-7.823589704776.84519968152-0.06093032497930.1064906470710.0359607471605-0.03273849365410.1406498445820.09175172876540.0946357828627-0.15405452345-0.07701478026870.2933987690720.0419657074972-0.0527423850490.24280733392-0.03264307889010.331361943134-25.80123.994-23.595
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 11:369 )A11 - 369
2X-RAY DIFFRACTION2( CHAIN A AND RESID 402:402 )A402
3X-RAY DIFFRACTION3( CHAIN A AND RESID 403:403 )A403

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