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- PDB-7uep: PANK3 complex structure with compound PZ-3860 -

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Basic information

Entry
Database: PDB / ID: 7uep
TitlePANK3 complex structure with compound PZ-3860
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-Y93 / Pantothenate kinase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 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)43,0895
Polymers42,1261
Non-polymers9634
Water1,47782
1
A: Pantothenate kinase 3
hetero molecules

A: Pantothenate kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,17810
Polymers84,2522
Non-polymers1,9278
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area8520 Å2
ΔGint-51 kcal/mol
Surface area27800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.833, 98.833, 68.994
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, 86 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-Y93 / 1-[(2R)-4-(6-chloropyridazin-3-yl)-2-methylpiperazin-1-yl]-2-(4-cyclopropylphenyl)ethan-1-one


Mass: 370.876 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H23ClN4O / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.31 Å3/Da / Density % sol: 46.73 %
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: 26853 / % possible obs: 99.6 % / Redundancy: 6.2 % / Biso Wilson estimate: 37.77 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.08 / Net I/σ(I): 26.5
Reflection shellResolution: 2→2.04 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.805 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1653 / CC1/2: 0.791 / % possible all: 99.5

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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→36.37 Å / SU ML: 0.1992 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 21.0532 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2141 1303 4.92 %
Rwork0.1763 25204 -
obs0.1781 26507 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.1 Å2
Refinement stepCycle: LAST / Resolution: 2→36.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2739 0 62 82 2883
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00792859
X-RAY DIFFRACTIONf_angle_d0.96413871
X-RAY DIFFRACTIONf_chiral_restr0.0545430
X-RAY DIFFRACTIONf_plane_restr0.005488
X-RAY DIFFRACTIONf_dihedral_angle_d16.02331663
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.080.24651450.21752762X-RAY DIFFRACTION99.55
2.08-2.170.25791440.20872742X-RAY DIFFRACTION99.14
2.17-2.290.21721450.19562783X-RAY DIFFRACTION100
2.29-2.430.22651460.1812771X-RAY DIFFRACTION100
2.43-2.620.24381410.1832808X-RAY DIFFRACTION99.93
2.62-2.880.22251430.17942797X-RAY DIFFRACTION99.83
2.88-3.30.2511450.17912787X-RAY DIFFRACTION98.85
3.3-4.160.20511410.16462834X-RAY DIFFRACTION99.9
4.16-36.370.18541530.16962920X-RAY DIFFRACTION99.23
Refinement TLS params.Method: refined / Origin x: -22.1104404213 Å / Origin y: 21.8823440195 Å / Origin z: -6.06959412668 Å
111213212223313233
T0.248452961998 Å2-0.0255877101405 Å2-0.0227466798877 Å2-0.265256291864 Å2-0.00789937575397 Å2--0.227974081618 Å2
L2.31434826457 °20.656436748137 °2-1.20371783361 °2-1.53917924036 °2-0.498838045924 °2--2.01348041193 °2
S0.126791129416 Å °-0.387822096973 Å °0.000327272247258 Å °0.208127228847 Å °-0.15570875499 Å °0.104662037321 Å °-0.168204581547 Å °0.173461495792 Å °0.0287877960836 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 11 through 369)

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