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- PDB-6pg8: WDR5delta23 bound to (2-(3-phenylpropyl)-1H-imidazol-4-yl)methanol -

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Basic information

Entry
Database: PDB / ID: 6pg8
TitleWDR5delta23 bound to (2-(3-phenylpropyl)-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 ...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 / regulation of cell division / Formation of WDR5-containing histone-modifying complexes / 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
[2-(3-phenylpropyl)-1H-imidazol-4-yl]methanol / WD repeat-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 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
C: WD repeat-containing protein 5
D: WD repeat-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,89513
Polymers137,7924
Non-polymers1,1039
Water15,961886
1
A: WD repeat-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7003
Polymers34,4481
Non-polymers2522
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)34,7603
Polymers34,4481
Non-polymers3122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: WD repeat-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7003
Polymers34,4481
Non-polymers2522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: WD repeat-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7354
Polymers34,4481
Non-polymers2873
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.118, 75.831, 79.239
Angle α, β, γ (deg.)104.70, 96.41, 105.23
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPAA31 - 33311 - 313
21ASPASPBB31 - 33311 - 313
12CYSCYSAA31 - 33411 - 314
22CYSCYSCC31 - 33411 - 314
13CYSCYSAA31 - 33411 - 314
23CYSCYSDD31 - 33411 - 314
14ASPASPBB31 - 33311 - 313
24ASPASPCC31 - 33311 - 313
15ASPASPBB31 - 33311 - 313
25ASPASPDD31 - 33311 - 313
16CYSCYSCC31 - 33411 - 314
26CYSCYSDD31 - 33411 - 314

NCS ensembles :
ID
1
2
3
4
5
6

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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.: 4
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-OGY / [2-(3-phenylpropyl)-1H-imidazol-4-yl]methanol


Mass: 216.279 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H16N2O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 886 / 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: 2.16 Å3/Da / Density % sol: 43.11 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop
Details: 0.179 M ammonium sulfate, 0.1 M bis-tris chloride (pH 5.62), 28.6 %w/v PEG3350

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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: Jul 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.67→46.71 Å / Num. obs: 128452 / % possible obs: 96.4 % / Redundancy: 3.8 % / CC1/2: 0.999 / Net I/σ(I): 11.3
Reflection shellResolution: 1.67→1.7 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2 / Num. unique obs: 6091 / CC1/2: 0.751 / % possible all: 92.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6PG3

6pg3


Resolution: 1.67→46.71 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.96 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.105 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20678 6204 4.8 %RANDOM
Rwork0.18683 ---
obs0.18782 122246 96.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.039 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å2-0.5 Å20.12 Å2
2---0.61 Å20.21 Å2
3---0.38 Å2
Refinement stepCycle: 1 / Resolution: 1.67→46.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9419 0 73 886 10378
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0139920
X-RAY DIFFRACTIONr_bond_other_d0.0360.0179067
X-RAY DIFFRACTIONr_angle_refined_deg1.4071.63313483
X-RAY DIFFRACTIONr_angle_other_deg2.3451.59321200
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.08651258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.38424.845386
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.255151700
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7521511
X-RAY DIFFRACTIONr_chiral_restr0.070.21312
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211043
X-RAY DIFFRACTIONr_gen_planes_other0.0090.021986
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_it1.3281.8524981
X-RAY DIFFRACTIONr_mcbond_other1.3261.8524980
X-RAY DIFFRACTIONr_mcangle_it2.0052.7686256
X-RAY DIFFRACTIONr_mcangle_other2.0062.7696257
X-RAY DIFFRACTIONr_scbond_it1.7892.0944939
X-RAY DIFFRACTIONr_scbond_other1.7862.0914936
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8333.0377222
X-RAY DIFFRACTIONr_long_range_B_refined4.30521.91410991
X-RAY DIFFRACTIONr_long_range_B_other4.30521.91310992
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A104920.05
12B104920.05
21A104270.06
22C104270.06
31A104460.06
32D104460.06
41B102750.06
42C102750.06
51B102870.06
52D102870.06
61C104970.05
62D104970.05
LS refinement shellResolution: 1.67→1.717 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 436 -
Rwork0.287 8785 -
obs--93.04 %

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