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- PDB-7uev: PANK3 complex structure with compound PZ-4200 -

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Basic information

Entry
Database: PDB / ID: 7uev
TitlePANK3 complex structure with compound PZ-4200
ComponentsPantothenate kinase 3
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / PANK / Transferase / Inhibitor / Activator / TRANSFERASE-TRANSFERASE INHIBITOR complex
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-N0I / Pantothenate kinase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWhite, S.W. / Yun, M. / Lee, R.E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Discovery of hPANK Activators with Improved Pharmacological Properties
Authors: Tangallapally, R. / Edwards, A. / Subramanian, C. / Sharma, L.K. / Yun, M. / White, S.W. / Jackowski, S. / Rock, C.O. / 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

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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)43,2377
Polymers42,1261
Non-polymers1,1116
Water2,216123
1
A: Pantothenate kinase 3
hetero molecules

A: Pantothenate kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,47314
Polymers84,2522
Non-polymers2,22212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area9180 Å2
ΔGint-70 kcal/mol
Surface area27890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.233, 98.233, 69.096
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 , 7 types, 129 molecules

#2: Chemical ChemComp-N0I / N-(4-{2-[4-(6-chloropyridazin-3-yl)piperazin-1-yl]-2-oxoethyl}phenyl)-N-methylmethanesulfonamide


Mass: 423.917 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H22ClN5O3S / 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-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.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.28 Å3/Da / Density % sol: 46.16 %
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: Oct 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 35739 / % possible obs: 99.9 % / Redundancy: 8.5 % / Biso Wilson estimate: 27.97 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.029 / Rrim(I) all: 0.085 / Net I/σ(I): 31.7
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 8.4 % / Rmerge(I) obs: 1.099 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2224 / CC1/2: 0.818 / CC star: 0.949 / Rpim(I) all: 0.4 / % possible all: 99.9

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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: PDB 6B3V

6b3v


Resolution: 1.8→40.03 Å / SU ML: 0.1855 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 19.4941 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2107 1774 4.97 %
Rwork0.1762 33938 -
obs0.1779 35712 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.62 Å2
Refinement stepCycle: LAST / Resolution: 1.8→40.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2709 0 69 123 2901
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00932841
X-RAY DIFFRACTIONf_angle_d1.17443850
X-RAY DIFFRACTIONf_chiral_restr0.0683423
X-RAY DIFFRACTIONf_plane_restr0.0063486
X-RAY DIFFRACTIONf_dihedral_angle_d10.82571649
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.25741350.23312550X-RAY DIFFRACTION98.39
1.85-1.910.21881360.21092589X-RAY DIFFRACTION99.93
1.91-1.970.25481330.18842587X-RAY DIFFRACTION99.96
1.97-2.040.21381390.17872606X-RAY DIFFRACTION100
2.04-2.120.21021370.18132559X-RAY DIFFRACTION100
2.12-2.220.24611330.18482601X-RAY DIFFRACTION100
2.22-2.330.20211380.17652594X-RAY DIFFRACTION100
2.33-2.480.20521330.17872610X-RAY DIFFRACTION100
2.48-2.670.23971360.17482620X-RAY DIFFRACTION100
2.67-2.940.19291320.1812611X-RAY DIFFRACTION99.78
2.94-3.370.25181390.17682624X-RAY DIFFRACTION100
3.37-4.240.18291400.15862658X-RAY DIFFRACTION99.96
4.24-40.030.19751430.1762729X-RAY DIFFRACTION99.1
Refinement TLS params.Method: refined / Origin x: -29.950648641 Å / Origin y: -7.98369669936 Å / Origin z: 4.98888301964 Å
111213212223313233
T0.207527125305 Å20.0113013984426 Å2-0.00481832602629 Å2-0.160869760456 Å2-0.00806425263271 Å2--0.142197180884 Å2
L1.15670673068 °20.215354419435 °2-0.384601456186 °2-2.22748383691 °2-0.991708546875 °2--1.77877956803 °2
S0.0039583999979 Å °-0.110538197412 Å °-0.0838478426771 Å °0.385633807692 Å °-0.0365573769054 Å °0.0448954005334 Å °-0.137058703023 Å °-0.00523105197789 Å °0.0205180386622 Å °
Refinement TLS groupSelection details: all

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