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- PDB-9clq: PANK3 complex structure with compound PZ-4352 -

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Basic information

Entry
Database: PDB / ID: 9clq
TitlePANK3 complex structure with compound PZ-4352
ComponentsPantothenate kinase 3
KeywordsTRANSFERASE / PANK / Substrate / Complex / 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 / Pantothenate kinase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsYun, M. / Lee, R.E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: PANK3 complex structure with compound PZ-4352
Authors: Yun, M. / Lee, R.E.
History
DepositionJul 12, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 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)43,3008
Polymers42,1261
Non-polymers1,1747
Water2,720151
1
A: Pantothenate kinase 3
hetero molecules

A: Pantothenate kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,60016
Polymers84,2522
Non-polymers2,34814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area10970 Å2
ΔGint-27 kcal/mol
Surface area27600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.836, 97.836, 69.292
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, 158 molecules

#2: Chemical ChemComp-A1AZA / 2-(4-cyclopropyl-2-fluorophenyl)-1-[4-(6-fluoro[1,3]oxazolo[4,5-b]pyridin-2-yl)piperazin-1-yl]ethan-1-one


Mass: 398.406 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H20F2N4O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION


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


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: 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
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.27 Å3/Da / Density % sol: 45.88 %
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: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.85→34.65 Å / Num. obs: 33027 / % possible obs: 100 % / Redundancy: 15.4 % / Biso Wilson estimate: 24.95 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.12 / Net I/σ(I): 15.3
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 14 % / Rmerge(I) obs: 1.314 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2006 / CC1/2: 0.768 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
autoPROC1.0.5data reduction
Aimless0.7.9data scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→32.07 Å / SU ML: 0.1711 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.1345 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2169 1652 5.01 %
Rwork0.1881 31335 -
obs0.1896 32987 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.24 Å2
Refinement stepCycle: LAST / Resolution: 1.85→32.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2734 0 77 151 2962
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00362866
X-RAY DIFFRACTIONf_angle_d0.72613876
X-RAY DIFFRACTIONf_chiral_restr0.0449425
X-RAY DIFFRACTIONf_plane_restr0.0039490
X-RAY DIFFRACTIONf_dihedral_angle_d9.72811661
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90.27941380.25412583X-RAY DIFFRACTION99.89
1.9-1.970.23671370.21912567X-RAY DIFFRACTION99.93
1.97-2.040.25441360.20282597X-RAY DIFFRACTION100
2.04-2.120.18841380.2022562X-RAY DIFFRACTION100
2.12-2.210.24721370.19752605X-RAY DIFFRACTION100
2.21-2.330.23881340.19022584X-RAY DIFFRACTION100
2.33-2.480.20821330.1892602X-RAY DIFFRACTION100
2.48-2.670.21881400.19162619X-RAY DIFFRACTION99.96
2.67-2.940.20391330.19092590X-RAY DIFFRACTION100
2.94-3.360.20991390.18212636X-RAY DIFFRACTION99.96
3.36-4.230.20831440.17172641X-RAY DIFFRACTION99.96
4.23-32.070.2111430.18322749X-RAY DIFFRACTION99.79
Refinement TLS params.Method: refined / Origin x: -29.8244161688 Å / Origin y: -8.05082401173 Å / Origin z: 5.1404782403 Å
111213212223313233
T0.155950164889 Å20.0223061820255 Å2-0.00946014585892 Å2-0.122174335954 Å2-0.00473769699814 Å2--0.124935021995 Å2
L1.05449463425 °20.245317951565 °2-0.312297937109 °2-1.51432623731 °2-0.665723247426 °2--1.58767548327 °2
S-0.0279401073892 Å °-0.0774222689512 Å °-0.0861322491103 Å °0.271972628978 Å °-0.029088994607 Å °0.00879010754674 Å °-0.0969247846012 Å °0.00343594015267 Å °0.0448301162864 Å °
Refinement TLS groupSelection details: all

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