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- PDB-9d2o: PANK3 complex structure with compound PZ-5351 -

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Basic information

Entry
Database: PDB / ID: 9d2o
TitlePANK3 complex structure with compound PZ-5351
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
: / ACETIC ACID / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Pantothenate kinase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsYun, M. / Lee, R.E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: 2-(4-aminophenyl)acetamide derivatives as Pantothenate Kinase Inhibitors.
Authors: Yun, M. / Lee, R.E.
History
DepositionAug 9, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

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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)43,2827
Polymers42,1261
Non-polymers1,1576
Water2,396133
1
A: Pantothenate kinase 3
hetero molecules

A: Pantothenate kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,56514
Polymers84,2522
Non-polymers2,31312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area9150 Å2
ΔGint-43 kcal/mol
Surface area27630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.544, 97.544, 69.250
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, 139 molecules

#2: Chemical ChemComp-A1A1N / N-(4-{2-[4-(6-chloropyridazin-3-yl)piperazin-1-yl]-2-oxoethyl}-3-fluorophenyl)ethanesulfonamide


Mass: 441.907 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H21ClFN5O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#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: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.26 Å3/Da / Density % sol: 45.52 %
Crystal growTemperature: 293 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: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jan 31, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 1.8→34.63 Å / Num. obs: 35586 / % possible obs: 100 % / Redundancy: 12.1 % / Biso Wilson estimate: 27.23 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.088 / Net I/σ(I): 16.5
Reflection shellResolution: 1.8→1.84 Å / Rmerge(I) obs: 1.287 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2072 / CC1/2: 0.756

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
autoPROC1.0.5data processing
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→32.04 Å / SU ML: 0.1774 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.248 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2003 1839 5.17 %
Rwork0.1811 33716 -
obs0.1821 35555 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.17 Å2
Refinement stepCycle: LAST / Resolution: 1.8→32.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2704 0 73 133 2910
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00862831
X-RAY DIFFRACTIONf_angle_d1.03683831
X-RAY DIFFRACTIONf_chiral_restr0.0648422
X-RAY DIFFRACTIONf_plane_restr0.0057482
X-RAY DIFFRACTIONf_dihedral_angle_d11.9871639
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.27221150.24312585X-RAY DIFFRACTION100
1.85-1.90.26821300.22242567X-RAY DIFFRACTION99.96
1.9-1.960.22541400.19972579X-RAY DIFFRACTION99.96
1.96-2.030.20491520.1892554X-RAY DIFFRACTION100
2.03-2.120.25691450.18662559X-RAY DIFFRACTION99.96
2.12-2.210.191280.17512583X-RAY DIFFRACTION100
2.21-2.330.21181390.17882577X-RAY DIFFRACTION100
2.33-2.470.20681450.17782572X-RAY DIFFRACTION100
2.47-2.670.21711560.17372591X-RAY DIFFRACTION100
2.67-2.930.22241310.18052599X-RAY DIFFRACTION100
2.93-3.360.19831580.1822588X-RAY DIFFRACTION100
3.36-4.230.1771440.16592643X-RAY DIFFRACTION99.93
4.23-32.040.1811560.18412719X-RAY DIFFRACTION99.9
Refinement TLS params.Method: refined / Origin x: -29.9156674467 Å / Origin y: -7.78950555072 Å / Origin z: 4.95647140828 Å
111213212223313233
T0.186979712311 Å20.0219604455344 Å2-0.00332170489375 Å2-0.156548476511 Å2-0.00287519530319 Å2--0.151443466008 Å2
L1.00702225694 °20.117529252894 °2-0.322763560973 °2-1.58032293795 °2-0.620887994386 °2--1.37941781376 °2
S-0.0226721434258 Å °-0.112980751994 Å °-0.0791252018131 Å °0.293415067128 Å °-0.016525929291 Å °0.0420530745165 Å °-0.0818737861189 Å °0.0333403701267 Å °0.0275275697085 Å °
Refinement TLS groupSelection details: all

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