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- PDB-7ueq: PANK3 complex structure with compound PZ-4061 -

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Basic information

Entry
Database: PDB / ID: 7ueq
TitlePANK3 complex structure with compound PZ-4061
ComponentsPantothenate kinase 3
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / PANK / Transferase / Inhibitor / Activator / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


Coenzyme A biosynthesis / vitamin binding / acetyl-CoA 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-N06 / Pantothenate kinase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 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)43,0164
Polymers42,1261
Non-polymers8903
Water2,702150
1
A: Pantothenate kinase 3
hetero molecules

A: Pantothenate kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,0328
Polymers84,2522
Non-polymers1,7816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area8070 Å2
ΔGint-58 kcal/mol
Surface area27710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.827, 97.827, 68.927
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

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Components

#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
#2: 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
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-N06 / 1-[4-(6-chloropyridazin-3-yl)piperazin-1-yl]-2-[4-(dimethylamino)phenyl]ethan-1-one


Mass: 359.853 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H22ClN5O / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O
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: 2.26 Å3/Da / Density % sol: 45.58 %
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-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 42082 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 25.78 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.023 / Rrim(I) all: 0.061 / Net I/σ(I): 36.4
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.642 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 2607 / CC1/2: 0.904 / CC star: 0.974 / Rpim(I) all: 0.263 / Rrim(I) all: 0.695 / % possible all: 99.9

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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: PDB 6B3V

6b3v


Resolution: 1.7→42.36 Å / SU ML: 0.1677 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.423 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2147 1996 4.75 %
Rwork0.176 40049 -
obs0.1778 42045 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.16 Å2
Refinement stepCycle: LAST / Resolution: 1.7→42.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2716 0 57 150 2923
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00562831
X-RAY DIFFRACTIONf_angle_d0.91933833
X-RAY DIFFRACTIONf_chiral_restr0.0533421
X-RAY DIFFRACTIONf_plane_restr0.0052484
X-RAY DIFFRACTIONf_dihedral_angle_d7.72151644
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.25321420.22672817X-RAY DIFFRACTION98.18
1.74-1.790.26321390.20342816X-RAY DIFFRACTION99.97
1.79-1.840.24031380.19612859X-RAY DIFFRACTION99.93
1.84-1.90.22411410.19612835X-RAY DIFFRACTION99.83
1.9-1.970.21081430.1842834X-RAY DIFFRACTION99.97
1.97-2.050.19811420.17922816X-RAY DIFFRACTION100
2.05-2.140.23131480.18052862X-RAY DIFFRACTION100
2.14-2.260.20311410.18052846X-RAY DIFFRACTION100
2.26-2.40.24591440.1812849X-RAY DIFFRACTION99.9
2.4-2.580.23441380.18082854X-RAY DIFFRACTION99.93
2.58-2.840.20751410.17582876X-RAY DIFFRACTION99.8
2.84-3.250.21871440.18012885X-RAY DIFFRACTION99.87
3.25-4.10.2141440.15832894X-RAY DIFFRACTION99.84
4.1-42.360.19581510.17243006X-RAY DIFFRACTION99.56
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)
11.918473817580.28984870094-0.9120241435290.992104016697-0.1129238389081.591846803490.0950526914615-0.282581360419-0.004301647656150.163562162976-0.1261227967750.10055262851-0.06278459477250.1001882661660.02178220113740.190933215861-0.0314217830887-0.005142689680370.1704788950190.004802173155990.150219982636-21.93522.111-6.213
22.000068422390.819806446506-0.7473823633384.456932432512.16816673463.496597727310.0418063559916-0.0978608765201-0.1998170473590.0426107887552-0.09171402229520.04712660428340.1968268837180.1150009586020.07234526450160.212106280420.003997944822390.01585379133940.213654578210.02051937616110.227316092611-21.82116.091-9.777
39.498460043482.001822912151.995381904171.994696040921.995336397011.99755004529-0.5045890322320.7548582900290.0135677147272-0.05272566073310.2790580126150.109799994956-0.147241415996-0.4470289439810.2385491679430.3284652462780.01521326427260.009145169277080.281942443746-0.03202504290330.287031712712-25.87124.336-23.84
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 501:501 )A501
3X-RAY DIFFRACTION3( CHAIN A AND RESID 503:503 )A503

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