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- PDB-6pgc: WDR5delta32 bound to methyl benzyl(4-(4-(hydroxymethyl)-1H-imidaz... -

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Basic information

Entry
Database: PDB / ID: 6pgc
TitleWDR5delta32 bound to methyl benzyl(4-(4-(hydroxymethyl)-1H-imidazol-2-yl)butyl)carbamate
ComponentsWD repeat-containing protein 5
KeywordsPROTEIN BINDING/INHIBITOR / Inhibitor / Scaffolding Protein / B-propellor / Chromatin regulator / PROTEIN BINDING-INHIBITOR complex
Function / homology
Function and homology information


histone H3Q5ser reader activity / histone H3K4me1 reader activity / Epigenetic regulation of gene expression by MLL3 and MLL4 complexes / MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / Cardiogenesis ...histone H3Q5ser reader activity / histone H3K4me1 reader activity / Epigenetic regulation of gene expression by MLL3 and MLL4 complexes / MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / Cardiogenesis / Formation of WDR5-containing histone-modifying complexes / histone methyltransferase complex / regulation of cell division / MLL1 complex / regulation of embryonic development / histone acetyltransferase complex / positive regulation of gluconeogenesis / transcription initiation-coupled chromatin remodeling / gluconeogenesis / skeletal system development / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / PKMTs methylate histone lysines / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / mitotic spindle / Neddylation / HATs acetylate histones / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / 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
WDR5 beta-propeller domain / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. ...WDR5 beta-propeller domain / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD domain, G-beta repeat / G-protein beta WD-40 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 / Mainly Beta
Similarity search - Domain/homology
Chem-OJJ / WD repeat-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsDennis, M.L. / Peat, T.S.
CitationJournal: Struct Dyn. / Year: 2019
Title: Fragment screening for a protein-protein interaction inhibitor to WDR5.
Authors: Dennis, M.L. / Morrow, B.J. / Dolezal, O. / Cuzzupe, A.N. / Stupple, A.E. / Newman, J. / Bentley, J. / Hattarki, M. / Nuttall, S.D. / Foitzik, R.C. / Street, I.P. / Stupple, P.A. / Monahan, B.J. / Peat, T.S.
History
DepositionJun 24, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)34,0474
Polymers33,5371
Non-polymers5103
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area330 Å2
ΔGint-22 kcal/mol
Surface area11730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.716, 65.285, 97.173
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein WD repeat-containing protein 5 / WDR5 / BMP2-induced 3-kb gene protein


Mass: 33537.016 Da / Num. of mol.: 1 / Fragment: UNP residues 32-334
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR5, BIG3 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P61964
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-OJJ / methyl benzyl{4-[4-(hydroxymethyl)-1H-imidazol-2-yl]butyl}carbamate


Mass: 317.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H23N3O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.21 Å3/Da / Density % sol: 44.32 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop
Details: 0.237 M ammonium sulfate, 0.1 M Bis-Tris chloride, pH 6.92, 25.7% w/v MPEG5000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.81→46.72 Å / Num. obs: 27580 / % possible obs: 99.2 % / Redundancy: 7.2 % / CC1/2: 0.999 / Net I/σ(I): 17.1
Reflection shellResolution: 1.81→1.85 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 2.6 / Num. unique obs: 1402 / CC1/2: 0.791 / % possible all: 87

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6PG4

6pg4


Resolution: 1.81→42.14 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.921 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.145 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2477 1383 5 %RANDOM
Rwork0.20302 ---
obs0.20529 26139 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.431 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å2-0 Å2
2---1.47 Å2-0 Å2
3---1.64 Å2
Refinement stepCycle: 1 / Resolution: 1.81→42.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2360 0 33 200 2593
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132477
X-RAY DIFFRACTIONr_bond_other_d0.0360.0172266
X-RAY DIFFRACTIONr_angle_refined_deg1.4371.6363361
X-RAY DIFFRACTIONr_angle_other_deg2.3541.5995297
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.095310
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.96824.84597
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.08215427
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.764153
X-RAY DIFFRACTIONr_chiral_restr0.0610.2325
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022732
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02490
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3822.1741234
X-RAY DIFFRACTIONr_mcbond_other1.3822.1731233
X-RAY DIFFRACTIONr_mcangle_it2.1533.2551546
X-RAY DIFFRACTIONr_mcangle_other2.1523.2561547
X-RAY DIFFRACTIONr_scbond_it1.5572.3681243
X-RAY DIFFRACTIONr_scbond_other1.5562.3691244
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4233.4761816
X-RAY DIFFRACTIONr_long_range_B_refined3.86425.3662751
X-RAY DIFFRACTIONr_long_range_B_other3.86425.3682752
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.815→1.862 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 110 -
Rwork0.285 1845 -
obs--97.22 %

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