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- PDB-7ue7: PANK3 complex structure with compound PZ-3883 -

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Basic information

Entry
Database: PDB / ID: 7ue7
TitlePANK3 complex structure with compound PZ-3883
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-NE3 / Pantothenate kinase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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)43,1436
Polymers42,1261
Non-polymers1,0175
Water2,684149
1
A: Pantothenate kinase 3
hetero molecules

A: Pantothenate kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,28612
Polymers84,2522
Non-polymers2,03410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area9060 Å2
ΔGint-53 kcal/mol
Surface area27470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.213, 98.213, 69.240
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, 154 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-NE3 / 6-{4-[(4-cyclopropyl-3-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.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.29 Å3/Da / Density % sol: 46.25 %
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: RAYONIX MX300-HS / Detector: CCD / Date: Nov 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 56098 / % possible obs: 99.8 % / Redundancy: 8 % / Biso Wilson estimate: 24.92 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.094 / Net I/σ(I): 28.1
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.857 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3455 / CC1/2: 0.67 / % possible all: 98.6

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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: 1.55→32.15 Å / SU ML: 0.1794 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.311 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1963 2004 3.57 %
Rwork0.1798 54053 -
obs0.1804 56057 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.06 Å2
Refinement stepCycle: LAST / Resolution: 1.55→32.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2710 0 67 149 2926
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00562878
X-RAY DIFFRACTIONf_angle_d0.94263901
X-RAY DIFFRACTIONf_chiral_restr0.055428
X-RAY DIFFRACTIONf_plane_restr0.0046491
X-RAY DIFFRACTIONf_dihedral_angle_d17.7241677
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.590.3081350.27863764X-RAY DIFFRACTION98.19
1.59-1.630.26361420.25573821X-RAY DIFFRACTION99.92
1.63-1.680.29051420.22833829X-RAY DIFFRACTION100
1.68-1.730.21821390.20473851X-RAY DIFFRACTION99.92
1.73-1.80.21061410.19633847X-RAY DIFFRACTION100
1.8-1.870.19981430.18613835X-RAY DIFFRACTION100
1.87-1.950.21421420.18423834X-RAY DIFFRACTION99.95
1.95-2.060.20271440.183848X-RAY DIFFRACTION100
2.06-2.180.2231450.18043887X-RAY DIFFRACTION100
2.18-2.350.1741410.18173836X-RAY DIFFRACTION100
2.35-2.590.22891450.18433885X-RAY DIFFRACTION100
2.59-2.960.22291450.18343893X-RAY DIFFRACTION100
2.96-3.730.18081440.16773928X-RAY DIFFRACTION100
3.73-32.150.16951560.16853995X-RAY DIFFRACTION98.67
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)
11.639297418390.275013687495-0.7841549746310.902559081838-0.210481836111.502751110110.071179485138-0.231786405645-0.01208610511220.113202157146-0.106603956620.0725181145058-0.06939738055320.09147297078030.03371677477950.174411423141-0.0222343647137-0.01016332195150.169559104117-0.001267238667270.157464129861-21.83822.182-6.282
22.13123530449-0.1330895425550.05197573250264.743147648631.057899105044.33024325670.0570887160479-0.0481410156606-0.140397581711-0.04601781920250.05045916909280.05718382859160.1355358518630.0296677427195-0.02752309981570.195952657336-4.01739510335E-50.01545097064870.2167075031220.003444973470210.242494153034-21.85216.092-9.815
30.0787804697821-0.1305343937240.2779934774440.2248992367-0.4727426934370.997348414268-0.06014289719310.02997049639450.01070790571930.007762763925320.04851513216120.04016374870890.0418511307779-0.01288308710781.085394100940.367183446468-0.045382559601-0.01126001323240.380352922368-0.05705620857090.378920177273-25.92423.953-23.425
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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