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- PDB-4ia9: Crystal structure of human WD REPEAT DOMAIN 5 in complex with 2-c... -

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Basic information

Entry
Database: PDB / ID: 4ia9
TitleCrystal structure of human WD REPEAT DOMAIN 5 in complex with 2-chloro-4-fluoro-3-methyl-N-[2-(4-methylpiperazin-1-yl)-5-nitrophenyl]benzamide
ComponentsWD repeat-containing protein 5
KeywordsTRANSCRIPTION / WDR5 / STRUCTURAL GENOMICS CONSORTIUM / WD REPEAT DOMAIN 5 / SGC
Function / homology
Function and homology information


MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / : / Cardiogenesis / histone methyltransferase complex / regulation of tubulin deacetylation ...MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / : / Cardiogenesis / histone methyltransferase complex / regulation of tubulin deacetylation / Formation of WDR5-containing histone-modifying complexes / regulation of cell division / MLL1 complex / regulation of embryonic development / histone acetyltransferase complex / positive regulation of gluconeogenesis / transcription initiation-coupled chromatin remodeling / methylated histone binding / skeletal system development / gluconeogenesis / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / mitotic spindle / PKMTs methylate histone lysines / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Neddylation / HATs acetylate histones / histone binding / regulation of cell cycle / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. ...YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Chem-IA9 / WD repeat-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsDong, A. / Dombrovski, L. / Bolshan, Y. / Getlik, M. / Tempel, W. / Kuznetsova, E. / Wasney, G.A. / Hajian, T. / Poda, G. / Nguyen, K.T. ...Dong, A. / Dombrovski, L. / Bolshan, Y. / Getlik, M. / Tempel, W. / Kuznetsova, E. / Wasney, G.A. / Hajian, T. / Poda, G. / Nguyen, K.T. / Schapira, M. / Brown, P.J. / Al-awar, R. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Smil, D. / Vedadi, M. / Wu, H. / Structural Genomics Consortium (SGC)
CitationJournal: ACS Med Chem Lett / Year: 2013
Title: Synthesis, Optimization, and Evaluation of Novel Small Molecules as Antagonists of WDR5-MLL Interaction.
Authors: Bolshan, Y. / Getlik, M. / Kuznetsova, E. / Wasney, G.A. / Hajian, T. / Poda, G. / Nguyen, K.T. / Wu, H. / Dombrovski, L. / Dong, A. / Senisterra, G. / Schapira, M. / Arrowsmith, C.H. / ...Authors: Bolshan, Y. / Getlik, M. / Kuznetsova, E. / Wasney, G.A. / Hajian, T. / Poda, G. / Nguyen, K.T. / Wu, H. / Dombrovski, L. / Dong, A. / Senisterra, G. / Schapira, M. / Arrowsmith, C.H. / Brown, P.J. / Al-Awar, R. / Vedadi, M. / Smil, D.
History
DepositionDec 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: WD repeat-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,82128
Polymers34,2901
Non-polymers53127
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.800, 86.029, 40.917
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein WD repeat-containing protein 5 / BMP2-induced 3-kb gene protein


Mass: 34289.887 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR5, BIG3 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) V2RpRARE / References: UniProt: P61964
#2: Chemical ChemComp-IA9 / 2-chloro-4-fluoro-3-methyl-N-[2-(4-methylpiperazin-1-yl)-5-nitrophenyl]benzamide


Mass: 406.839 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H20ClFN4O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 24 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O

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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: 2.07 Å3/Da / Density % sol: 40.68 %
Crystal growTemperature: 291 K / pH: 5.5
Details: 25% PEH 3500, 0.1 M Ammonium sulfate, 0.1 M BisTris pH5.5, vapor diffusion hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97912 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97912 Å / Relative weight: 1
ReflectionResolution: 1.66→50 Å / Num. all: 34118 / Num. obs: 34118 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 15.6 Å2 / Rsym value: 0.069 / Net I/σ(I): 24.4
Reflection shellResolution: 1.66→1.69 Å / Mean I/σ(I) obs: 2.2 / Num. unique all: 1677 / Rsym value: 0.76 / % possible all: 97.8

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Processing

Software
NameVersionClassificationNB
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
MOLREP10.2..35phasing
Coot0.6.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SMR

3smr


Resolution: 1.66→33.63 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 1.905 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2103 1075 3.2 %RANDOM
Rwork0.1771 ---
all0.1781 33008 --
obs0.1781 34083 98.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 55.32 Å2 / Biso mean: 19.8741 Å2 / Biso min: 11.75 Å2
Baniso -1Baniso -2Baniso -3
1--1.3 Å20 Å20 Å2
2--0.25 Å2-0 Å2
3---1.05 Å2
Refinement stepCycle: LAST / Resolution: 1.66→33.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2320 0 60 250 2630
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.022473
X-RAY DIFFRACTIONr_bond_other_d0.0040.022289
X-RAY DIFFRACTIONr_angle_refined_deg1.2951.9493382
X-RAY DIFFRACTIONr_angle_other_deg0.9073.0045294
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0995325
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.15525.21792
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.62515403
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.434153
X-RAY DIFFRACTIONr_chiral_restr0.0650.2385
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022812
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02553
LS refinement shellResolution: 1.66→1.704 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 75 -
Rwork0.249 2374 -
all-2449 -
obs--96.72 %

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