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- PDB-6x4l: PANK3 complex structure with compound PZ-3565 -

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Basic information

Entry
Database: PDB / ID: 6x4l
TitlePANK3 complex structure with compound PZ-3565
ComponentsPantothenate kinase 3
KeywordsTRANSFERASE / PANK / Substrate / Complex / Pantothenate kinase
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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Chem-UOS / Pantothenate kinase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWhite, S.W. / Yun, M.
CitationJournal: Bioorg.Med.Chem. / Year: 2021
Title: LipE guided discovery of isopropylphenyl pyridazines as pantothenate kinase modulators.
Authors: Sharma, L.K. / Yun, M.K. / Subramanian, C. / Tangallapally, R. / Jackowski, S. / Rock, C.O. / White, S.W. / Lee, R.E.
History
DepositionMay 22, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 8, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 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)43,1757
Polymers42,1261
Non-polymers1,0496
Water1,802100
1
A: Pantothenate kinase 3
hetero molecules

A: Pantothenate kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,34914
Polymers84,2522
Non-polymers2,09812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area9320 Å2
ΔGint-54 kcal/mol
Surface area27420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.514, 98.514, 68.820
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, 106 molecules

#2: Chemical ChemComp-UOS / 1-[4-(5-chloropyrazin-2-yl)piperazin-1-yl]-2-[4-(propan-2-yl)phenyl]ethan-1-one


Mass: 358.865 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H23ClN4O / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.29 Å3/Da / Density % sol: 46.25 %
Crystal growTemperature: 291.15 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: 1.004 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.004 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 26579 / % possible obs: 100 % / Redundancy: 5.6 % / Biso Wilson estimate: 37.91 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.09 / Net I/σ(I): 20.4
Reflection shellResolution: 2→2.05 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.978 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1872 / CC1/2: 0.69 / % 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: 5KPR

5kpr


Resolution: 2→40.05 Å / SU ML: 0.2146 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.4266 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2176 1300 4.93 %
Rwork0.1761 25073 -
obs0.1782 26373 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.05 Å2
Refinement stepCycle: LAST / Resolution: 2→40.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2702 0 66 100 2868
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00672833
X-RAY DIFFRACTIONf_angle_d0.87423839
X-RAY DIFFRACTIONf_chiral_restr0.051427
X-RAY DIFFRACTIONf_plane_restr0.0046485
X-RAY DIFFRACTIONf_dihedral_angle_d17.46771652
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.080.31941450.22552749X-RAY DIFFRACTION100
2.08-2.170.27441370.21362750X-RAY DIFFRACTION99.97
2.17-2.290.23911400.19372767X-RAY DIFFRACTION100
2.29-2.430.23531460.18592751X-RAY DIFFRACTION99.9
2.43-2.620.26121450.1832762X-RAY DIFFRACTION100
2.62-2.880.2211460.17732772X-RAY DIFFRACTION100
2.88-3.30.22621480.17572783X-RAY DIFFRACTION99.97
3.3-4.160.19651410.16112828X-RAY DIFFRACTION99.87
4.16-40.050.19821520.17182911X-RAY DIFFRACTION99.93
Refinement TLS params.Method: refined / Origin x: -30.1427493583 Å / Origin y: -7.8847024441 Å / Origin z: 5.2611589444 Å
111213212223313233
T0.294471416919 Å20.0202968094188 Å20.000183505770552 Å2-0.250339931286 Å2-0.0123062207945 Å2--0.221274494024 Å2
L1.46967151388 °20.285700935797 °2-0.36503533156 °2-2.85839077976 °2-1.40103930862 °2--2.20924297985 °2
S0.00198569436253 Å °-0.167864227179 Å °-0.101578656681 Å °0.516218683054 Å °-0.0150165968834 Å °0.0940647121639 Å °-0.230644293469 Å °-0.0797993066579 Å °0.0184111221117 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 11 through 369)

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