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- PDB-7ue8: PANK3 complex structure with compound PZ-3890 -

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Basic information

Entry
Database: PDB / ID: 7ue8
TitlePANK3 complex structure with compound PZ-3890
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
ACETATE ION / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Chem-Y92 / Pantothenate kinase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsWhite, S.W. / Yun, M. / Lee, R.E.
Funding support United States, 1items
OrganizationGrant numberCountry
CoA Therapeutics, Inc. United States
CitationJournal: J Inherit Metab Dis / Year: 2023
Title: Relief of CoA sequestration and restoration of mitochondrial function in a mouse model of propionic acidemia.
Authors: Subramanian, C. / Frank, M.W. / Tangallapally, R. / Yun, M.K. / White, S.W. / Lee, R.E. / Rock, C.O. / Jackowski, S.
History
DepositionMar 21, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1May 10, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _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
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)43,1526
Polymers42,1261
Non-polymers1,0265
Water1,44180
1
A: Pantothenate kinase 3
hetero molecules

A: Pantothenate kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,30412
Polymers84,2522
Non-polymers2,05310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area9050 Å2
ΔGint-52 kcal/mol
Surface area28010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.571, 98.571, 68.941
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, 85 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-Y92 / 1-[4-(6-chloropyridazin-3-yl)piperazin-1-yl]-2-(4-cyclopropyl-3-fluorophenyl)ethan-1-one


Mass: 374.840 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H20ClFN4O / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.3 Å3/Da / Density % sol: 46.41 %
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: 2→50 Å / Num. obs: 26128 / % possible obs: 99.7 % / Redundancy: 5.7 % / Biso Wilson estimate: 38.03 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.069 / Net I/σ(I): 26.5
Reflection shellResolution: 2→2.04 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1601 / CC1/2: 0.689 / % possible all: 99.6

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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: 2.01→32.26 Å / SU ML: 0.1995 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.9312 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1995 1305 5 %
Rwork0.1744 24799 -
obs0.1758 26104 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.93 Å2
Refinement stepCycle: LAST / Resolution: 2.01→32.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2723 0 66 80 2869
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072846
X-RAY DIFFRACTIONf_angle_d0.88013850
X-RAY DIFFRACTIONf_chiral_restr0.0512425
X-RAY DIFFRACTIONf_plane_restr0.0053485
X-RAY DIFFRACTIONf_dihedral_angle_d17.12281658
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.090.25471370.23852651X-RAY DIFFRACTION97.93
2.09-2.180.29371410.22612752X-RAY DIFFRACTION99.66
2.18-2.30.22871440.19852726X-RAY DIFFRACTION99.76
2.3-2.440.25331410.18842731X-RAY DIFFRACTION99.79
2.44-2.630.22091420.17872746X-RAY DIFFRACTION99.86
2.63-2.890.20831460.17612776X-RAY DIFFRACTION100
2.89-3.310.20781470.1772742X-RAY DIFFRACTION99.48
3.31-4.170.18291510.15722795X-RAY DIFFRACTION99.97
4.17-32.260.17421560.1662880X-RAY DIFFRACTION99.48
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)
11.91270428751-0.345285141474-0.8273621891842.758133199360.08015418952282.8122321962-0.111029078294-0.349537946771-0.388912793760.6702213752370.01449970762060.1345394501670.08240039858450.1499226981690.09591026662020.4332069300590.0204222140271-0.0005079510600080.299297773630.0701175070590.343809793087-29.442-19.83913.765
21.96630332610.810503968443-0.6344288742193.09537378717-1.587436235652.468799632420.00676248660712-0.05248674090030.1889922289660.386421137134-0.01697097474050.116585736945-0.388145647554-0.123051629218-0.004778015400280.3183176232790.0441883554669-0.008805378083420.215551718278-0.0195533449590.229351534337-30.8411.447-1.426
36.13965320077-1.497912013956.164101813693.05950559144-0.3406084348836.70005632858-0.39497234573-0.1975702124580.113870230918-0.4627545898970.06680564412490.101096399915-0.1740894843420.1582333319720.3057383761970.715313940351-0.005498187987640.1506559937350.481244626338-0.04394163777130.565745839285-33.916-10.259-12.065
43.637084211933.70354379182-2.258206073567.26359523722.707216623088.591146387020.192754214953-0.0486019814754-0.164052391133-0.409974669490.09785723236040.0448232916056-0.1132394523140.0171687818044-0.2360160590140.327632120914-0.0309098224892-0.008383688389640.3417889927880.00794353654760.389779410311-24.892-10.9341.749
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 11:172 )A11 - 172
2X-RAY DIFFRACTION2( CHAIN A AND RESID 173:369 )A173 - 369
3X-RAY DIFFRACTION3( CHAIN A AND RESID 503:503 )A503
4X-RAY DIFFRACTION4( CHAIN A AND RESID 501:501 )A501

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