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- PDB-9d2p: PANK3 complex structure with compound PZ-4127 -

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Basic information

Entry
Database: PDB / ID: 9d2p
TitlePANK3 complex structure with compound PZ-4127
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
ACETIC ACID / ADENOSINE-5'-DIPHOSPHATE / Chem-MZI / Pantothenate kinase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsYun, M. / Lee, R.E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: 2-(4-aminophenyl)acetamide derivatives as Pantothenate Kinase Inhibitors.
Authors: Yun, M. / Lee, R.E.
History
DepositionAug 9, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

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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)43,1316
Polymers42,1261
Non-polymers1,0055
Water2,144119
1
A: Pantothenate kinase 3
hetero molecules

A: Pantothenate kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,26212
Polymers84,2522
Non-polymers2,01110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area8050 Å2
ΔGint-59 kcal/mol
Surface area27650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.927, 97.927, 69.061
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, 124 molecules

#2: Chemical ChemComp-MZI / 2-(4-{2-[4-(6-chloropyridazin-3-yl)piperazin-1-yl]-2-oxoethyl}anilino)-2-oxoethyl acetate


Mass: 431.873 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H22ClN5O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#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.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 45.8 %
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: RAYONIX MX300-HS / Detector: CCD / Date: Oct 5, 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: 35665 / % possible obs: 100 % / Redundancy: 10.6 % / Biso Wilson estimate: 30 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.065 / Net I/σ(I): 24.3
Reflection shellResolution: 1.8→1.84 Å / Rmerge(I) obs: 1.046 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2201 / CC1/2: 0.722 / % 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 / Resolution: 1.8→48.96 Å / SU ML: 0.1862 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.1763 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2203 1774 4.98 %
Rwork0.1765 33859 -
obs0.1787 35633 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41 Å2
Refinement stepCycle: LAST / Resolution: 1.8→48.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2713 0 66 119 2898
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01292842
X-RAY DIFFRACTIONf_angle_d1.27463846
X-RAY DIFFRACTIONf_chiral_restr0.0832424
X-RAY DIFFRACTIONf_plane_restr0.0076488
X-RAY DIFFRACTIONf_dihedral_angle_d5.79852266
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.25261360.23822534X-RAY DIFFRACTION97.8
1.85-1.90.28451320.21882584X-RAY DIFFRACTION99.89
1.9-1.970.26161360.19752568X-RAY DIFFRACTION99.96
1.97-2.040.24061360.18482603X-RAY DIFFRACTION100
2.04-2.120.24171390.1792544X-RAY DIFFRACTION100
2.12-2.210.2191340.18062598X-RAY DIFFRACTION100
2.21-2.330.19671370.17472590X-RAY DIFFRACTION100
2.33-2.480.23941330.17382588X-RAY DIFFRACTION100
2.48-2.670.20251390.17042632X-RAY DIFFRACTION100
2.67-2.940.21461370.17362588X-RAY DIFFRACTION100
2.94-3.360.2281380.17332631X-RAY DIFFRACTION100
3.36-4.230.19591340.16372652X-RAY DIFFRACTION99.96
4.23-48.960.22571430.182747X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -29.8176336762 Å / Origin y: -7.88321188444 Å / Origin z: 5.02790870022 Å
111213212223313233
T0.225070241913 Å20.0286187106818 Å20.00118748340047 Å2-0.177969358897 Å2-0.00883751543644 Å2--0.169051013539 Å2
L1.40600217355 °20.302481411117 °2-0.435521024554 °2-2.27678555753 °2-1.02760637511 °2--2.13260761697 °2
S-0.0320931645056 Å °-0.161593371321 Å °-0.104703896129 Å °0.419574239725 Å °-0.0145147489095 Å °0.055716812697 Å °-0.139686906369 Å °-0.0211741254223 Å °0.0513918139517 Å °
Refinement TLS groupSelection details: all

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