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- PDB-7ue3: PANK3 complex structure with compound PZ-3804 -

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Basic information

Entry
Database: PDB / ID: 7ue3
TitlePANK3 complex structure with compound PZ-3804
ComponentsPantothenate kinase 3
KeywordsTRANSFERASE / PANK / Substrate / Complex / Pantothenate kinase / Inhibitor / Activator
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-ND6 / Pantothenate kinase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 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 21, 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)43,98713
Polymers42,1261
Non-polymers1,86112
Water3,927218
1
A: Pantothenate kinase 3
hetero molecules

A: Pantothenate kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,97326
Polymers84,2522
Non-polymers3,72224
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area11860 Å2
ΔGint-19 kcal/mol
Surface area27960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.198, 98.198, 69.169
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-712-

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 , 5 types, 230 molecules

#2: Chemical ChemComp-ND6 / 6-[4-({4-[(2R)-1-hydroxypropan-2-yl]phenyl}acetyl)piperazin-1-yl]pyridazine-3-carbonitrile


Mass: 365.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H23N5O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 46.18 %
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: 1.56→50 Å / Num. obs: 55022 / % possible obs: 100 % / Redundancy: 7.3 % / Biso Wilson estimate: 19.15 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Net I/σ(I): 34.9
Reflection shellResolution: 1.56→1.59 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.811 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3354 / CC1/2: 0.805 / % 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: 6B3V

6b3v


Resolution: 1.56→32.14 Å / SU ML: 0.1448 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.4439 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1961 2002 3.64 %
Rwork0.1687 52984 -
obs0.1697 54986 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.97 Å2
Refinement stepCycle: LAST / Resolution: 1.56→32.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2720 0 119 218 3057
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00952894
X-RAY DIFFRACTIONf_angle_d1.22123912
X-RAY DIFFRACTIONf_chiral_restr0.0698432
X-RAY DIFFRACTIONf_plane_restr0.0066487
X-RAY DIFFRACTIONf_dihedral_angle_d17.81371677
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.56-1.60.24761420.22543717X-RAY DIFFRACTION99.48
1.6-1.640.24721430.20333746X-RAY DIFFRACTION100
1.64-1.690.22091430.19063757X-RAY DIFFRACTION100
1.69-1.740.21651400.1833725X-RAY DIFFRACTION99.9
1.74-1.810.19561460.17693766X-RAY DIFFRACTION99.97
1.81-1.880.22111440.16913775X-RAY DIFFRACTION100
1.88-1.970.19391440.16063755X-RAY DIFFRACTION99.97
1.97-2.070.20111420.15553760X-RAY DIFFRACTION99.97
2.07-2.20.20221430.15913767X-RAY DIFFRACTION100
2.2-2.370.16671410.16253784X-RAY DIFFRACTION100
2.37-2.610.1731450.16563806X-RAY DIFFRACTION100
2.61-2.980.19161440.17273809X-RAY DIFFRACTION100
2.98-3.760.20661400.16563847X-RAY DIFFRACTION100
3.76-32.140.19081450.16693970X-RAY DIFFRACTION99.98
Refinement TLS params.Method: refined / Origin x: -30.0500337031 Å / Origin y: -7.84762309837 Å / Origin z: 5.28865163031 Å
111213212223313233
T0.143008687779 Å20.00365084039331 Å2-0.00413104673501 Å2-0.123228946284 Å2-0.0050303395702 Å2--0.110206718247 Å2
L0.599054479795 °20.17107955452 °2-0.182974701222 °2-1.50304860886 °2-0.710095855377 °2--1.18549578138 °2
S0.00103307320439 Å °-0.0787199826715 Å °-0.0787645161143 Å °0.25992986418 Å °-0.0409393808287 Å °0.000502397172954 Å °-0.0697116850525 Å °-0.00552384119502 Å °0.0337568033072 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 11 through 369)

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