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- PDB-8bw2: PanDDA analysis -- Crystal Structure of PHIP in complex with Z198... -

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Basic information

Entry
Database: PDB / ID: 8bw2
TitlePanDDA analysis -- Crystal Structure of PHIP in complex with Z198194396 synthetic derivative
ComponentsPH-interacting protein
KeywordsSIGNALING PROTEIN / brodomain / automated chemistry / reaction product
Function / homology
Function and homology information


regulation of cell morphogenesis / positive regulation of insulin-like growth factor receptor signaling pathway / regulation of protein phosphorylation / histone reader activity / RHOBTB2 GTPase cycle / cytoskeleton organization / positive regulation of mitotic nuclear division / negative regulation of extrinsic apoptotic signaling pathway / insulin receptor binding / insulin receptor signaling pathway ...regulation of cell morphogenesis / positive regulation of insulin-like growth factor receptor signaling pathway / regulation of protein phosphorylation / histone reader activity / RHOBTB2 GTPase cycle / cytoskeleton organization / positive regulation of mitotic nuclear division / negative regulation of extrinsic apoptotic signaling pathway / insulin receptor binding / insulin receptor signaling pathway / regulation of cell shape / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
: / : / : / BRWD/PHIP ancillary domain-like domain / BRWD1-like, N-terminal domain / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain ...: / : / : / BRWD/PHIP ancillary domain-like domain / BRWD1-like, N-terminal domain / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / WD domain, G-beta repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Chem-Y3Y / PH-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsGrosjean, H. / Aimon, A. / Hassell-Hart, S. / Bradshaw, W.J. / Krojer, T. / Talon, R. / Douangamath, A. / Koekemoer, L. / Biggin, P.C. / Spencer, J. / von Delft, F.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2025
Title: Binding-Site Purification of Actives (B-SPA) Enables Efficient Large-Scale Progression of Fragment Hits by Combining Multi-Step Array Synthesis With HT Crystallography.
Authors: Grosjean, H. / Aimon, A. / Hassell-Hart, S. / Thompson, W. / Koekemoer, L. / Bennett, J. / Bradley, A. / Anderson, C. / Wild, C. / Bradshaw, W.J. / FitzGerald, E.A. / Krojer, T. / Fedorov, O. ...Authors: Grosjean, H. / Aimon, A. / Hassell-Hart, S. / Thompson, W. / Koekemoer, L. / Bennett, J. / Bradley, A. / Anderson, C. / Wild, C. / Bradshaw, W.J. / FitzGerald, E.A. / Krojer, T. / Fedorov, O. / Biggin, P.C. / Spencer, J. / von Delft, F.
History
DepositionDec 6, 2022Deposition site: PDBE / Processing site: PDBE
SupersessionDec 21, 2022ID: 5S9F
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2Jan 28, 2026Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PH-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9392
Polymers17,6281
Non-polymers3111
Water2,450136
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Biological assembly 1 assigned by authors and generated by PISA (software)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.570, 26.886, 55.645
Angle α, β, γ (deg.)90.000, 100.304, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1730-

HOH

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Components

#1: Protein PH-interacting protein / PHIP / DDB1- and CUL4-associated factor 14 / IRS-1 PH domain-binding protein / WD repeat-containing protein 11


Mass: 17627.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PHIP, DCAF14, WDR11 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WWQ0
#2: Chemical ChemComp-Y3Y / (2R)-N-(2-methoxyethyl)-2-methyl-4-thiophen-2-ylcarbonyl-piperazine-1-carboxamide


Mass: 311.400 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H21N3O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 1.7 Å3/Da / Density % sol: 27.71 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 20% PEG 8000, 0.04M POTASSIUM PHOSPHATE

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9127 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9127 Å / Relative weight: 1
ReflectionResolution: 1.35→54.75 Å / Num. obs: 26051 / % possible obs: 98.3 % / Redundancy: 2.8 % / CC1/2: 0.996 / Net I/σ(I): 7.2
Reflection shellResolution: 1.35→1.37 Å / Mean I/σ(I) obs: 0.5 / Num. unique obs: 1196 / CC1/2: 0.413

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7AV9

7av9


Resolution: 1.35→54.748 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.485 / SU ML: 0.09 / Cross valid method: FREE R-VALUE / ESU R: 0.079 / ESU R Free: 0.078
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2576 1322 5.081 %
Rwork0.1994 24697 -
all0.202 --
obs-26019 98.129 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 21.32 Å2
Baniso -1Baniso -2Baniso -3
1-0.099 Å2-0 Å20.827 Å2
2--0.603 Å20 Å2
3----0.941 Å2
Refinement stepCycle: LAST / Resolution: 1.35→54.748 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms990 0 21 136 1147
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0121062
X-RAY DIFFRACTIONr_bond_other_d0.0050.016943
X-RAY DIFFRACTIONr_angle_refined_deg1.4941.6671439
X-RAY DIFFRACTIONr_angle_other_deg0.4851.5662212
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.135126
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.939512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.31410186
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.1621053
X-RAY DIFFRACTIONr_chiral_restr0.0660.2151
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021229
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02223
X-RAY DIFFRACTIONr_nbd_refined0.2350.2247
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1950.2900
X-RAY DIFFRACTIONr_nbtor_refined0.1940.2544
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.2527
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.290
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0030.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1840.226
X-RAY DIFFRACTIONr_nbd_other0.1520.261
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.230.226
X-RAY DIFFRACTIONr_mcbond_it3.1022.021492
X-RAY DIFFRACTIONr_mcbond_other3.1012.021492
X-RAY DIFFRACTIONr_mcangle_it3.9333.047619
X-RAY DIFFRACTIONr_mcangle_other3.9383.05620
X-RAY DIFFRACTIONr_scbond_it4.5732.601570
X-RAY DIFFRACTIONr_scbond_other4.5692.603571
X-RAY DIFFRACTIONr_scangle_it5.423.729819
X-RAY DIFFRACTIONr_scangle_other5.4173.737820
X-RAY DIFFRACTIONr_lrange_it5.90238.7271342
X-RAY DIFFRACTIONr_lrange_other5.75535.0651305
X-RAY DIFFRACTIONr_rigid_bond_restr4.54132005
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.35-1.3850.41680.42417350.42419300.370.42893.41970.417
1.385-1.4230.41080.38916220.3919000.8180.81791.05260.383
1.423-1.4640.341110.33717160.33818470.8930.89798.91720.333
1.464-1.5090.343990.29616560.29817790.8910.91398.65090.287
1.509-1.5590.2861020.25815970.25917240.920.9498.54990.243
1.559-1.6130.288770.21315860.21616880.9420.96598.5190.2
1.613-1.6740.26790.19515430.19916270.9650.97599.69270.185
1.674-1.7420.286910.18214500.18815510.9490.97899.35530.167
1.742-1.820.22560.18914420.1915040.9650.97799.60110.173
1.82-1.9090.303690.23513350.23814370.9270.9597.70350.218
1.909-2.0120.36690.27312740.27813560.9050.93599.04130.256
2.012-2.1340.227600.18612580.18813210.9630.97799.77290.173
2.134-2.2810.236500.22211540.22312180.9530.95798.85060.205
2.281-2.4630.277460.16510800.16911300.9570.98299.6460.158
2.463-2.6980.234670.1610040.16510720.9650.98399.90670.157
2.698-3.0150.224450.1698970.1729450.9690.98199.68250.169
3.015-3.480.236380.1798020.1818430.9650.98299.64410.181
3.48-4.2570.201360.1486930.157330.9770.98799.45430.156
4.257-6.0030.206350.1455260.1485670.9830.98998.94180.156
6.003-54.7480.239160.1733270.1763430.9740.9751000.19

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