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- PDB-8bw4: PanDDA analysis -- Crystal Structure of PHIP in complex with Z198... -

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Basic information

Entry
Database: PDB / ID: 8bw4
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 / 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 / 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 / Bromodomain (BrD) profile. / Bromodomain-like superfamily ...: / 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-Y3S / PH-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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: 5S9I
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

Downloads & links

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Assembly

Deposited unit
A: PH-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0052
Polymers17,6281
Non-polymers3771
Water2,702150
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)81.789, 27.009, 55.563
Angle α, β, γ (deg.)90.000, 99.944, 90.000
Int Tables number5
Space group name H-MC121

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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-Y3S / (2R)-4-(3-fluoranylthiophen-2-yl)carbonyl-N-(4-methoxyphenyl)-2-methyl-piperazine-1-carboxamide


Mass: 377.433 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H20FN3O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 1.71 Å3/Da / Density % sol: 28.03 %
Crystal growTemperature: 277.5 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: Oct 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9127 Å / Relative weight: 1
ReflectionResolution: 1.55→40.28 Å / Num. obs: 17568 / % possible obs: 99.2 % / Redundancy: 3 % / CC1/2: 0.96 / Net I/σ(I): 6
Reflection shellResolution: 1.55→1.58 Å / Mean I/σ(I) obs: 0.8 / Num. unique obs: 863 / CC1/2: 0.544

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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: 1.55→40.28 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.865 / SU B: 9.725 / SU ML: 0.148 / Cross valid method: FREE R-VALUE / ESU R: 0.164 / ESU R Free: 0.134
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3161 1078 6.139 %
Rwork0.2346 16483 -
all0.239 --
obs-17561 99.024 %
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: 19.628 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20 Å20.566 Å2
2--0.672 Å20 Å2
3----1.216 Å2
Refinement stepCycle: LAST / Resolution: 1.55→40.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms990 0 26 150 1166
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0121041
X-RAY DIFFRACTIONr_bond_other_d0.0080.016920
X-RAY DIFFRACTIONr_angle_refined_deg1.3891.6711406
X-RAY DIFFRACTIONr_angle_other_deg0.5141.5622151
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3345118
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.338512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.97810181
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.6761053
X-RAY DIFFRACTIONr_chiral_restr0.0630.2146
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021189
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02219
X-RAY DIFFRACTIONr_nbd_refined0.2490.2254
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2060.2876
X-RAY DIFFRACTIONr_nbtor_refined0.1920.2533
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.070.2535
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2102
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0850.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2490.235
X-RAY DIFFRACTIONr_nbd_other0.3010.281
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2040.230
X-RAY DIFFRACTIONr_mcbond_it3.8011.753475
X-RAY DIFFRACTIONr_mcbond_other3.7971.751475
X-RAY DIFFRACTIONr_mcangle_it4.5082.648592
X-RAY DIFFRACTIONr_mcangle_other4.5062.65593
X-RAY DIFFRACTIONr_scbond_it4.8252.42566
X-RAY DIFFRACTIONr_scbond_other4.8212.421567
X-RAY DIFFRACTIONr_scangle_it5.7013.46814
X-RAY DIFFRACTIONr_scangle_other5.6983.475815
X-RAY DIFFRACTIONr_lrange_it9.45442.5021349
X-RAY DIFFRACTIONr_lrange_other7.89839.1681301
X-RAY DIFFRACTIONr_rigid_bond_restr4.37131961
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.590.384720.3541220X-RAY DIFFRACTION98.1017
1.59-1.6340.373890.3191129X-RAY DIFFRACTION98.7835
1.634-1.6810.362690.2751159X-RAY DIFFRACTION99.6753
1.681-1.7330.323710.2681118X-RAY DIFFRACTION99.8321
1.733-1.7890.356610.2761093X-RAY DIFFRACTION98.886
1.789-1.8520.346660.2481019X-RAY DIFFRACTION97.7477
1.852-1.9220.442830.306992X-RAY DIFFRACTION97.8162
1.922-20.331640.281952X-RAY DIFFRACTION99.1219
2-2.0890.339870.241914X-RAY DIFFRACTION99.0109
2.089-2.190.26560.191890X-RAY DIFFRACTION99.789
2.19-2.3090.311570.203846X-RAY DIFFRACTION98.7965
2.309-2.4480.297520.222818X-RAY DIFFRACTION99.3151
2.448-2.6160.267490.286764X-RAY DIFFRACTION99.7546
2.616-2.8250.376460.24705X-RAY DIFFRACTION99.6021
2.825-3.0930.315330.206675X-RAY DIFFRACTION99.4382
3.093-3.4560.207280.2610X-RAY DIFFRACTION99.2224
3.456-3.9850.303350.196531X-RAY DIFFRACTION98.6063
3.985-4.8690.247230.176465X-RAY DIFFRACTION99.7955
4.869-6.8370.378250.215361X-RAY DIFFRACTION99.2288
6.837-40.280.176120.195222X-RAY DIFFRACTION100

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