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- PDB-7ue5: PANK3 complex structure with compound PZ-3741 -

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Basic information

Entry
Database: PDB / ID: 7ue5
TitlePANK3 complex structure with compound PZ-3741
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-Y88 / Chem-Y99 / Pantothenate kinase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 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 21, 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)43,4635
Polymers42,1261
Non-polymers1,3374
Water3,333185
1
A: Pantothenate kinase 3
hetero molecules

A: Pantothenate kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,92610
Polymers84,2522
Non-polymers2,6758
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area8100 Å2
ΔGint-59 kcal/mol
Surface area27730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.012, 98.012, 69.234
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

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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, 189 molecules

#2: Chemical ChemComp-Y88 / 6-[4-({4-[(2R)-1,1,1-trifluoropropan-2-yl]phenyl}acetyl)piperazin-1-yl]pyridazine-3-carbonitrile


Mass: 403.401 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H20F3N5O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-Y99 / 6-[4-({4-[(2S)-1,1,1-trifluoropropan-2-yl]phenyl}acetyl)piperazin-1-yl]pyridazine-3-carbonitrile


Mass: 403.401 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H20F3N5O / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#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


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.28 Å3/Da / Density % sol: 46.02 %
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: Jun 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.63→50 Å / Num. obs: 48301 / % possible obs: 99.8 % / Redundancy: 9.1 % / Biso Wilson estimate: 22.1 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Net I/σ(I): 37.6
Reflection shellResolution: 1.63→1.67 Å / Redundancy: 7.6 % / Rmerge(I) obs: 1.095 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2976 / CC1/2: 0.678 / % possible all: 99.2

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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: 1.63→32.08 Å / SU ML: 0.1614 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.8524 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1967 2006 4.17 %
Rwork0.1765 46113 -
obs0.1773 48119 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.32 Å2
Refinement stepCycle: LAST / Resolution: 1.63→32.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2717 0 61 185 2963
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062875
X-RAY DIFFRACTIONf_angle_d0.92493900
X-RAY DIFFRACTIONf_chiral_restr0.0523429
X-RAY DIFFRACTIONf_plane_restr0.0046489
X-RAY DIFFRACTIONf_dihedral_angle_d11.08622289
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.670.29861450.26133266X-RAY DIFFRACTION99.39
1.67-1.720.2541420.24073251X-RAY DIFFRACTION99.62
1.72-1.770.24671400.20893287X-RAY DIFFRACTION99.77
1.77-1.820.24411420.20573230X-RAY DIFFRACTION99.67
1.82-1.890.22941430.19663283X-RAY DIFFRACTION99.91
1.89-1.960.1971410.17733221X-RAY DIFFRACTION99.85
1.96-2.050.20221450.16563274X-RAY DIFFRACTION100
2.05-2.160.2111410.1743291X-RAY DIFFRACTION99.97
2.16-2.30.1851410.16773283X-RAY DIFFRACTION100
2.3-2.470.18871430.1753296X-RAY DIFFRACTION100
2.47-2.720.19651430.17123310X-RAY DIFFRACTION100
2.72-3.120.1951430.17743301X-RAY DIFFRACTION100
3.12-3.930.17531460.16363359X-RAY DIFFRACTION100
3.93-32.080.18851510.17243461X-RAY DIFFRACTION99.94
Refinement TLS params.Method: refined / Origin x: -21.8468256391 Å / Origin y: 22.0989702165 Å / Origin z: -6.23854896932 Å
111213212223313233
T0.153265068713 Å2-0.0207362208968 Å2-0.00319400612363 Å2-0.15043706554 Å20.00370347506263 Å2--0.127867609158 Å2
L1.53960115873 °20.26635509961 °2-0.751059207056 °2-0.722886199352 °2-0.121574228347 °2--1.26603571315 °2
S0.0682637090434 Å °-0.24885259503 Å °-0.023391125824 Å °0.115244411074 Å °-0.100721927366 Å °0.0742769640494 Å °-0.037557838293 Å °0.0902200815752 Å °0.0226898641197 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 11 through 369)

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