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- PDB-7ues: PANK3 complex structure with compound PZ-4202 -

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Basic information

Entry
Database: PDB / ID: 7ues
TitlePANK3 complex structure with compound PZ-4202
ComponentsPantothenate kinase 3
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / PANK / Transferase / Inhibitor / Activator / TRANSFERASE-TRANSFERASE INHIBITOR complex
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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Chem-MXO / 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)43,0574
Polymers42,1261
Non-polymers9313
Water2,144119
1
A: Pantothenate kinase 3
hetero molecules

A: Pantothenate kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,1138
Polymers84,2522
Non-polymers1,8626
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area8110 Å2
ΔGint-59 kcal/mol
Surface area27850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.011, 98.011, 69.057
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

#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
#2: Chemical ChemComp-MXO / N-(4-{2-[4-(6-cyanopyridazin-3-yl)piperazin-1-yl]-2-oxoethyl}phenyl)methanesulfonamide


Mass: 400.455 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H20N6O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O
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: 2.27 Å3/Da / Density % sol: 45.89 %
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: Dec 8, 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: 35321 / % possible obs: 99.1 % / Redundancy: 11.8 % / Biso Wilson estimate: 28.78 Å2 / CC1/2: 0.987 / CC star: 0.997 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.027 / Rrim(I) all: 0.095 / Net I/σ(I): 33.7
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 11.9 % / Rmerge(I) obs: 1.235 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2164 / CC1/2: 0.854 / CC star: 0.96 / Rpim(I) all: 0.369 / % possible all: 98.4

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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→36.16 Å / SU ML: 0.1559 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.7869 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1972 1752 4.96 %
Rwork0.1697 33552 -
obs0.1711 35304 98.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.29 Å2
Refinement stepCycle: LAST / Resolution: 1.8→36.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2706 0 60 119 2885
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072861
X-RAY DIFFRACTIONf_angle_d0.91283886
X-RAY DIFFRACTIONf_chiral_restr0.0531429
X-RAY DIFFRACTIONf_plane_restr0.0046485
X-RAY DIFFRACTIONf_dihedral_angle_d10.05681649
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.25091210.22032384X-RAY DIFFRACTION91.83
1.85-1.90.21781320.20042547X-RAY DIFFRACTION98.46
1.9-1.960.19731360.18032539X-RAY DIFFRACTION98.35
1.96-2.040.19471370.17182552X-RAY DIFFRACTION98.61
2.04-2.120.19461300.1752559X-RAY DIFFRACTION99.19
2.12-2.210.21111360.16742580X-RAY DIFFRACTION99.34
2.21-2.330.22551340.16682568X-RAY DIFFRACTION98.97
2.33-2.480.19891330.16932587X-RAY DIFFRACTION99.31
2.48-2.670.17871370.17192616X-RAY DIFFRACTION99.57
2.67-2.930.22741370.16912596X-RAY DIFFRACTION99.6
2.93-3.360.22831400.17222623X-RAY DIFFRACTION99.75
3.36-4.230.16871370.15422655X-RAY DIFFRACTION100
4.23-36.160.18881420.17312746X-RAY DIFFRACTION99.59
Refinement TLS params.Method: refined / Origin x: -21.6785050067 Å / Origin y: 21.9939900114 Å / Origin z: -6.62857827808 Å
111213212223313233
T0.174656711866 Å2-0.0311726059308 Å20.00729487703799 Å2-0.171416932879 Å20.00224009109402 Å2--0.140466427911 Å2
L1.98028043247 °20.476046835372 °2-0.885515950836 °2-1.04535043269 °2-0.263985325113 °2--1.40283877992 °2
S0.10940802946 Å °-0.332538318339 Å °-0.00938677289323 Å °0.189475687937 Å °-0.134438699333 Å °0.0834526913362 Å °-0.0624697552748 Å °0.127130049049 Å °0.0238996559143 Å °
Refinement TLS groupSelection details: all

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