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- PDB-7ue4: PANK3 complex structure with compound PZ-3855 -

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Basic information

Entry
Database: PDB / ID: 7ue4
TitlePANK3 complex structure with compound PZ-3855
ComponentsPantothenate kinase 3
KeywordsTRANSFERASE / PANK / Substrate / Complex / Pantothenate kinase / Inhibitor / Activator
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
ACETATE ION / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Chem-Y89 / Pantothenate kinase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsWhite, S.W. / Yun, M. / Lee, R.E.
Funding support United States, 1items
OrganizationGrant numberCountry
CoA Therapeutics, Inc. United States
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)43,1346
Polymers42,1261
Non-polymers1,0085
Water1,29772
1
A: Pantothenate kinase 3
hetero molecules

A: Pantothenate kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,26812
Polymers84,2522
Non-polymers2,01710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area8910 Å2
ΔGint-52 kcal/mol
Surface area27870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.598, 98.598, 68.965
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 , 6 types, 77 molecules

#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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-Y89 / 1-[4-(6-chloropyridazin-3-yl)piperazin-1-yl]-2-(4-cyclopropylphenyl)ethan-1-one


Mass: 356.849 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H21ClN4O / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.3 Å3/Da / Density % sol: 46.46 %
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: Aug 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.94→50 Å / Num. obs: 29091 / % possible obs: 99.7 % / Redundancy: 6.5 % / Biso Wilson estimate: 37.34 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.067 / Net I/σ(I): 34.4
Reflection shellResolution: 1.94→1.98 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.844 / Mean I/σ(I) obs: 2 / Num. unique obs: 1797 / CC1/2: 0.83

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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: 1.94→36.3 Å / SU ML: 0.2029 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.1136 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2194 1448 4.98 %
Rwork0.1776 27616 -
obs0.1797 29064 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.39 Å2
Refinement stepCycle: LAST / Resolution: 1.94→36.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2713 0 65 72 2850
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00642834
X-RAY DIFFRACTIONf_angle_d0.88513835
X-RAY DIFFRACTIONf_chiral_restr0.0511425
X-RAY DIFFRACTIONf_plane_restr0.005484
X-RAY DIFFRACTIONf_dihedral_angle_d19.10971651
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-20.28041440.24272722X-RAY DIFFRACTION99.44
2-2.080.25751460.20942714X-RAY DIFFRACTION99.86
2.08-2.180.26741410.20542730X-RAY DIFFRACTION99.17
2.18-2.290.24341370.19442763X-RAY DIFFRACTION99.97
2.29-2.440.20591430.19052737X-RAY DIFFRACTION100
2.44-2.630.22261450.18392748X-RAY DIFFRACTION100
2.63-2.890.22541520.17962766X-RAY DIFFRACTION99.66
2.89-3.310.19681430.18032749X-RAY DIFFRACTION99.35
3.31-4.170.20271460.16112806X-RAY DIFFRACTION99.83
4.17-36.30.22491510.17032881X-RAY DIFFRACTION99.05
Refinement TLS params.Method: refined / Origin x: -21.977231688 Å / Origin y: 22.1193962354 Å / Origin z: -6.16327193747 Å
111213212223313233
T0.244186665584 Å2-0.034752469762 Å2-0.00991177145551 Å2-0.245471219632 Å2-0.000383130682809 Å2--0.213627517017 Å2
L2.54742737686 °20.518642590727 °2-1.15837081868 °2-1.45965980903 °2-0.304530461925 °2--1.98515711752 °2
S0.129324627675 Å °-0.414403695576 Å °0.0135246658039 Å °0.209171732778 Å °-0.166931637255 Å °0.110239876271 Å °-0.131500972545 Å °0.141240088142 Å °0.034005311492 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 11 through 369)

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