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- PDB-7ue6: PANK3 complex structure with compound PZ-3802 -

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Basic information

Entry
Database: PDB / ID: 7ue6
TitlePANK3 complex structure with compound PZ-3802
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
ACETATE ION / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Chem-NDK / Pantothenate kinase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsWhite, S.W. / Yun, M. / Lee, R.E.
Funding support1items
OrganizationGrant numberCountry
Not funded
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 21, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 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)43,2708
Polymers42,1261
Non-polymers1,1447
Water3,513195
1
A: Pantothenate kinase 3
hetero molecules

A: Pantothenate kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,54016
Polymers84,2522
Non-polymers2,28814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area10170 Å2
ΔGint-36 kcal/mol
Surface area27120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.837, 97.837, 69.166
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
Components on special symmetry positions
IDModelComponents
11A-693-

HOH

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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, 202 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-NDK / 6-(4-{[5-fluoro-6-(propan-2-yl)pyridin-3-yl]acetyl}piperazin-1-yl)pyridazine-3-carbonitrile


Mass: 368.408 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H21FN6O / Feature type: SUBJECT OF INVESTIGATION
#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.: 195 / 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: 45.78 %
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-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.74→50 Å / Num. obs: 39378 / % possible obs: 99.6 % / Redundancy: 5 % / Biso Wilson estimate: 21.28 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.036 / Rrim(I) all: 0.083 / Net I/σ(I): 23.4
Reflection shellResolution: 1.74→1.78 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.843 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2436 / CC1/2: 0.712 / CC star: 0.912 / Rpim(I) all: 0.414 / Rrim(I) all: 0.941 / % possible all: 100

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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: 1.74→32.02 Å / SU ML: 0.2078 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 19.5752 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2047 1983 5.04 %
Rwork0.1789 37388 -
obs0.1802 39371 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.25 Å2
Refinement stepCycle: LAST / Resolution: 1.74→32.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2723 0 75 195 2993
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00592852
X-RAY DIFFRACTIONf_angle_d0.92933854
X-RAY DIFFRACTIONf_chiral_restr0.0541422
X-RAY DIFFRACTIONf_plane_restr0.0048486
X-RAY DIFFRACTIONf_dihedral_angle_d12.01261652
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.780.3441400.26022665X-RAY DIFFRACTION100
1.78-1.830.24841390.23392616X-RAY DIFFRACTION100
1.83-1.890.27651410.21842688X-RAY DIFFRACTION100
1.89-1.950.2311380.18992627X-RAY DIFFRACTION99.96
1.95-2.020.22071410.18122656X-RAY DIFFRACTION100
2.02-2.10.22611440.182681X-RAY DIFFRACTION100
2.1-2.190.21491380.18032630X-RAY DIFFRACTION100
2.19-2.310.21531430.17182678X-RAY DIFFRACTION99.96
2.31-2.450.17831430.17322672X-RAY DIFFRACTION99.86
2.45-2.640.20121390.16412658X-RAY DIFFRACTION99.75
2.64-2.910.19761460.1762692X-RAY DIFFRACTION99.58
2.91-3.330.20861450.17342691X-RAY DIFFRACTION99.44
3.33-4.190.17661440.1652677X-RAY DIFFRACTION98.77
4.19-32.020.19221420.18052757X-RAY DIFFRACTION97.74
Refinement TLS params.Method: refined / Origin x: -21.6596930687 Å / Origin y: 21.8891261932 Å / Origin z: -6.52017435422 Å
111213212223313233
T0.133602806292 Å2-0.0147466512029 Å2-0.00938493796537 Å2-0.126884916266 Å20.00541110000813 Å2--0.11775987835 Å2
L1.45513906917 °20.269537279077 °2-0.751875103975 °2-0.740793387575 °2-0.135402875419 °2--1.31396085556 °2
S0.0477586985259 Å °-0.212101999439 Å °-0.0309696613382 Å °0.103839342359 Å °-0.0909324361478 Å °0.0629412963523 Å °-0.0293518808142 Å °0.083758159314 Å °0.0336647306743 Å °
Refinement TLS groupSelection details: all

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