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- PDB-6x4j: PANK3 complex structure with compound PZ-2863 -

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Basic information

Entry
Database: PDB / ID: 6x4j
TitlePANK3 complex structure with compound PZ-2863
ComponentsPantothenate kinase 3
KeywordsTRANSFERASE / PANK / Substrate / Complex / Pantothenate kinase
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-UOM / Pantothenate kinase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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

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Assembly

Deposited unit
A: Pantothenate kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0675
Polymers42,1261
Non-polymers9414
Water1,22568
1
A: Pantothenate kinase 3
hetero molecules

A: Pantothenate kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,13410
Polymers84,2522
Non-polymers1,8828
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area8530 Å2
ΔGint-52 kcal/mol
Surface area27430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.428, 98.428, 68.922
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 , 5 types, 72 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#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-UOM / 6-(4-{[4-(propan-2-yl)phenyl]acetyl}piperazin-1-yl)pyridine-3-carbonitrile


Mass: 348.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H24N4O / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 46.24 %
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-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 17454 / % possible obs: 99.8 % / Redundancy: 6.2 % / Biso Wilson estimate: 40.47 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.103 / Net I/σ(I): 20.2
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.996 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1225 / CC1/2: 0.603 / % 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: 2.3→36.25 Å / SU ML: 0.3008 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.4648 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2356 871 5 %
Rwork0.1983 16561 -
obs0.2003 17432 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.45 Å2
Refinement stepCycle: LAST / Resolution: 2.3→36.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2705 0 62 68 2835
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00282823
X-RAY DIFFRACTIONf_angle_d0.60073824
X-RAY DIFFRACTIONf_chiral_restr0.0411424
X-RAY DIFFRACTIONf_plane_restr0.0031484
X-RAY DIFFRACTIONf_dihedral_angle_d15.94341641
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.440.32581430.27522715X-RAY DIFFRACTION99.97
2.44-2.630.28151410.24182736X-RAY DIFFRACTION100
2.63-2.90.25851430.21792743X-RAY DIFFRACTION100
2.9-3.320.22311460.20862754X-RAY DIFFRACTION99.97
3.32-4.180.21731460.17472755X-RAY DIFFRACTION99.9
4.18-36.250.22381520.18322858X-RAY DIFFRACTION99.31
Refinement TLS params.Method: refined / Origin x: 21.9526384887 Å / Origin y: -22.1340525467 Å / Origin z: -6.21079835775 Å
111213212223313233
T0.283161220362 Å2-0.0323964951717 Å20.0191673810828 Å2-0.268308411716 Å2-0.00801903484139 Å2--0.245133687541 Å2
L2.73031014428 °20.681420855117 °21.41556954833 °2-1.52168693875 °20.366763800731 °2--2.30370388481 °2
S0.146857961702 Å °-0.400511884447 Å °0.00734236946306 Å °0.221379962347 Å °-0.174114153297 Å °-0.127233566081 Å °0.142822747787 Å °-0.15465085023 Å °0.0173934629097 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 11 through 369)

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