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- PDB-6pg3: WDR5delta23 bound to (2-butyl-1H-imidazol-4-yl)methanol -

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Basic information

Entry
Database: PDB / ID: 6pg3
TitleWDR5delta23 bound to (2-butyl-1H-imidazol-4-yl)methanol
ComponentsWD repeat-containing protein 5
KeywordsPROTEIN BINDING/Inhibitor / Inhibitor / Scaffolding Protein / B-propellor / Chromatin regulator / PROTEIN BINDING / PROTEIN BINDING-Inhibitor complex
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 / Formation of WDR5-containing histone-modifying complexes ...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 / regulation of embryonic development / MLL1 complex / histone acetyltransferase complex / positive regulation of gluconeogenesis / methylated histone binding / transcription initiation-coupled chromatin remodeling / 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. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats ...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. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
(2-butyl-1H-imidazol-4-yl)methanol / WD repeat-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
B: WD repeat-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,2054
Polymers68,8962
Non-polymers3082
Water6,612367
1
A: WD repeat-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6022
Polymers34,4481
Non-polymers1541
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: WD repeat-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6022
Polymers34,4481
Non-polymers1541
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)112.825, 46.850, 129.154
Angle α, β, γ (deg.)90.00, 112.81, 90.00
Int Tables number5
Space group name H-MI121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: CYS / End label comp-ID: CYS / Refine code: _ / Auth seq-ID: 31 - 334 / Label seq-ID: 11 - 314

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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


Mass: 34448.047 Da / Num. of mol.: 2
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-OHJ / (2-butyl-1H-imidazol-4-yl)methanol


Mass: 154.210 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H14N2O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 367 / 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: 2.28 Å3/Da / Density % sol: 46.14 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop
Details: 0.182 M ammonium fluoride, 0.1 M sodium cacodylate (pH 5.79), 22.1 %w/v PEG8000

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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: Aug 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.04→43.63 Å / Num. obs: 39721 / % possible obs: 99.6 % / Redundancy: 7.4 % / CC1/2: 0.994 / Net I/σ(I): 10.3
Reflection shellResolution: 2.04→2.1 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 2.7 / Num. unique obs: 2912 / CC1/2: 0.866 / % possible all: 94.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2H9L

2h9l


Resolution: 2.04→43.63 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.938 / Cross valid method: THROUGHOUT / ESU R: 0.193 / ESU R Free: 0.157 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20617 1887 4.8 %RANDOM
Rwork0.173 ---
obs0.17459 37833 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 17.693 Å2
Baniso -1Baniso -2Baniso -3
1-1.94 Å2-0 Å20.1 Å2
2--0.04 Å20 Å2
3----1.53 Å2
Refinement stepCycle: 1 / Resolution: 2.04→43.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4650 0 22 367 5039
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0134817
X-RAY DIFFRACTIONr_bond_other_d0.0360.0174438
X-RAY DIFFRACTIONr_angle_refined_deg1.3921.6296535
X-RAY DIFFRACTIONr_angle_other_deg2.3391.59210365
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2635606
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.76224.624186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.88115831
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.201156
X-RAY DIFFRACTIONr_chiral_restr0.060.2639
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025312
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02956
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_it1.1231.7312421
X-RAY DIFFRACTIONr_mcbond_other1.1221.7312420
X-RAY DIFFRACTIONr_mcangle_it1.8072.5853028
X-RAY DIFFRACTIONr_mcangle_other1.8062.5863029
X-RAY DIFFRACTIONr_scbond_it1.5771.9562396
X-RAY DIFFRACTIONr_scbond_other1.5771.9562397
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5732.8373508
X-RAY DIFFRACTIONr_long_range_B_refined4.11920.1915341
X-RAY DIFFRACTIONr_long_range_B_other4.11920.1915342
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 10206 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.04→2.096 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 130 -
Rwork0.231 2635 -
obs--94.5 %

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