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- PDB-9g91: Crystal structure of HRP-2 PWWP domain in complex with compound 43 -

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Basic information

Entry
Database: PDB / ID: 9g91
TitleCrystal structure of HRP-2 PWWP domain in complex with compound 43
ComponentsHepatoma-derived growth factor-related protein 2
KeywordsGENE REGULATION / Inhibitor
Function / homology
Function and homology information


histone H3K27me3 reader activity / skeletal muscle tissue regeneration / histone H3K9me2/3 reader activity / muscle cell differentiation / muscle organ development / DNA repair-dependent chromatin remodeling / histone reader activity / positive regulation of double-strand break repair via homologous recombination / positive regulation of cell growth / DNA recombination ...histone H3K27me3 reader activity / skeletal muscle tissue regeneration / histone H3K9me2/3 reader activity / muscle cell differentiation / muscle organ development / DNA repair-dependent chromatin remodeling / histone reader activity / positive regulation of double-strand break repair via homologous recombination / positive regulation of cell growth / DNA recombination / chromatin remodeling / DNA repair / nucleus / cytoplasm
Similarity search - Function
Lens epithelium-derived growth factor, integrase-binding domain / HIV integrase-binding domain superfamily / Lens epithelium-derived growth factor (LEDGF) / TFIIS/LEDGF domain superfamily / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain
Similarity search - Domain/homology
: / Hepatoma-derived growth factor-related protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsVantieghem, T. / Osipov, E.M. / Strelkov, S.V.
Funding support Belgium, 3items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)1SC9822N Belgium
Research Foundation - Flanders (FWO)1SC9824N Belgium
Research Foundation - Flanders (FWO)G053822N Belgium
CitationJournal: Eur.J.Med.Chem. / Year: 2024
Title: Rational fragment-based design of compounds targeting the PWWP domain of the HRP family.
Authors: Vantieghem, T. / Aslam, N.A. / Osipov, E.M. / Akele, M. / Van Belle, S. / Beelen, S. / Drexler, M. / Paulovcakova, T. / Lux, V. / Fearon, D. / Douangamath, A. / von Delft, F. / Christ, F. / ...Authors: Vantieghem, T. / Aslam, N.A. / Osipov, E.M. / Akele, M. / Van Belle, S. / Beelen, S. / Drexler, M. / Paulovcakova, T. / Lux, V. / Fearon, D. / Douangamath, A. / von Delft, F. / Christ, F. / Veverka, V. / Verwilst, P. / Van Aerschot, A. / Debyser, Z. / Strelkov, S.V.
History
DepositionJul 24, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release

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Structure visualization

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MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hepatoma-derived growth factor-related protein 2
B: Hepatoma-derived growth factor-related protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,71712
Polymers21,3962
Non-polymers1,32110
Water4,432246
1
A: Hepatoma-derived growth factor-related protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2465
Polymers10,6981
Non-polymers5474
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hepatoma-derived growth factor-related protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4727
Polymers10,6981
Non-polymers7736
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.056, 41.663, 72.179
Angle α, β, γ (deg.)90.00, 102.84, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-317-

HOH

21A-326-

HOH

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Components

#1: Protein Hepatoma-derived growth factor-related protein 2 / HDGF-related protein 2 / HRP-2 / Hepatoma-derived growth factor 2 / HDGF-2


Mass: 10698.171 Da / Num. of mol.: 2 / Mutation: C64S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HDGFL2, HDGF2, HDGFRP2, HRP2, UNQ785/PRO1604 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7Z4V5
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-A1II3 / [3-[(5-bromanylpyridin-3-yl)methylamino]phenyl]methanol


Mass: 293.159 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H13BrN2O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O
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: 2.67 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 28% PEG MME 2000 0.15 M ammonium sulfate 0.1 M sodium acetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976253 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976253 Å / Relative weight: 1
ReflectionResolution: 1.78→70.37 Å / Num. obs: 21823 / % possible obs: 99.9 % / Redundancy: 4.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.067 / Rrim(I) all: 0.145 / Χ2: 0.91 / Net I/σ(I): 9.6 / Num. measured all: 100197
Reflection shellResolution: 1.78→1.88 Å / % possible obs: 100 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.981 / Num. measured all: 14148 / Num. unique obs: 3148 / CC1/2: 0.611 / Rpim(I) all: 0.52 / Rrim(I) all: 1.115 / Χ2: 0.78 / Net I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
Aimlessdata scaling
XDSdata reduction
autoPROCdata processing
MOLREPphasing
PHENIX(1.21.1_5286: ???)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→36.55 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2056 1021 4.69 %
Rwork0.173 --
obs0.1746 21787 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.78→36.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1484 0 73 246 1803
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041633
X-RAY DIFFRACTIONf_angle_d0.5932221
X-RAY DIFFRACTIONf_dihedral_angle_d14.269614
X-RAY DIFFRACTIONf_chiral_restr0.046196
X-RAY DIFFRACTIONf_plane_restr0.005299
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.880.33171450.26962918X-RAY DIFFRACTION100
1.88-1.990.22191530.21842953X-RAY DIFFRACTION100
1.99-2.150.23871270.19062950X-RAY DIFFRACTION100
2.15-2.360.23071440.1842962X-RAY DIFFRACTION100
2.36-2.70.21281440.17352961X-RAY DIFFRACTION100
2.71-3.410.19681600.16142971X-RAY DIFFRACTION100
3.41-36.550.1671480.14373051X-RAY DIFFRACTION99

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