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- PDB-5eam: Crystal structure of human WDR5 in complex with compound 9o -

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Basic information

Entry
Database: PDB / ID: 5eam
TitleCrystal structure of human WDR5 in complex with compound 9o
ComponentsWD repeat-containing protein 5
KeywordsTranscription/Transcription inhibitor / WDR5 / compound 9o / Structural Genomics / Structural Genomics Consortium / SGC / Transcription-Transcription 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 / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / 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. / 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
Chem-5MN / WD repeat-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsDONG, A. / DOMBROVSKI, L. / SMIL, D. / GETLIK, M. / BOLSHAN, Y. / WALKER, J.R. / SENISTERRA, G. / PODA, G. / AL-AWAR, R. / SCHAPIRA, M. ...DONG, A. / DOMBROVSKI, L. / SMIL, D. / GETLIK, M. / BOLSHAN, Y. / WALKER, J.R. / SENISTERRA, G. / PODA, G. / AL-AWAR, R. / SCHAPIRA, M. / VEDADI, M. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / BROWN, P.J. / WU, H. / Structural Genomics Consortium (SGC)
CitationJournal: J. Med. Chem. / Year: 2016
Title: Structure-Based Optimization of a Small Molecule Antagonist of the Interaction Between WD Repeat-Containing Protein 5 (WDR5) and Mixed-Lineage Leukemia 1 (MLL1).
Authors: Getlik, M. / Smil, D. / Zepeda-Velazquez, C. / Bolshan, Y. / Poda, G. / Wu, H. / Dong, A. / Kuznetsova, E. / Marcellus, R. / Senisterra, G. / Dombrovski, L. / Hajian, T. / Kiyota, T. / ...Authors: Getlik, M. / Smil, D. / Zepeda-Velazquez, C. / Bolshan, Y. / Poda, G. / Wu, H. / Dong, A. / Kuznetsova, E. / Marcellus, R. / Senisterra, G. / Dombrovski, L. / Hajian, T. / Kiyota, T. / Schapira, M. / Arrowsmith, C.H. / Brown, P.J. / Vedadi, M. / Al-Awar, R.
History
DepositionOct 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1May 23, 2018Group: Data collection / Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
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_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 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
B: WD repeat-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,04436
Polymers68,5802
Non-polymers1,46534
Water5,909328
1
A: WD repeat-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,77614
Polymers34,2901
Non-polymers48713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: WD repeat-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,26822
Polymers34,2901
Non-polymers97821
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.939, 54.779, 64.011
Angle α, β, γ (deg.)107.170, 90.210, 112.610
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 34289.887 Da / Num. of mol.: 2 / Fragment: UNP residues 23-334
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

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Non-polymers , 6 types, 362 molecules

#2: Chemical ChemComp-5MN / ~{N}-[5-(1~{H}-indol-5-yl)-2-(4-methylpiperazin-1-yl)phenyl]-3-methyl-benzamide


Mass: 424.537 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H28N4O
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 25 / Source method: obtained synthetically
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 2.1 Å3/Da / Density % sol: 41.37 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 25% PEG3350, 0.1M NH4SO4, 0.1 M BisTris pH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jan 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 50164 / % possible obs: 96.5 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.068 / Rrim(I) all: 0.126 / Χ2: 1.067 / Net I/av σ(I): 12.466 / Net I/σ(I): 7.3 / Num. measured all: 162177
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.8330.43720290.7930.30.5330.65377.9
1.83-1.863.10.36924230.8360.2490.4470.69193.6
1.86-1.93.20.34325260.8580.230.4140.76896.7
1.9-1.943.20.29624720.8830.1970.3570.92296
1.94-1.983.20.2625250.90.1730.3140.89196.7
1.98-2.033.20.22425520.9370.1490.270.90296.8
2.03-2.083.20.2224660.930.1440.2641.00897
2.08-2.133.20.1925590.9510.1240.2281.00797.1
2.13-2.23.20.18225120.9560.1190.2181.03597.3
2.2-2.273.30.20825290.9330.1350.2491.24597.3
2.27-2.353.30.16325470.960.1050.1941.02997.6
2.35-2.443.30.15224980.9610.0980.1821.02597.8
2.44-2.553.30.13925560.9750.0890.1661.05497.8
2.55-2.693.30.11825620.9770.0760.1411.10698
2.69-2.863.30.10325510.9840.0660.1221.10498.2
2.86-3.083.30.08925620.9850.0570.1061.22298.4
3.08-3.393.30.07825640.9870.050.0931.3498.7
3.39-3.883.30.07525590.9850.0480.0891.46398.8
3.88-4.883.30.06425720.9910.0410.0761.29799.2
4.88-503.30.06826000.9870.0450.0821.35599.6

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Processing

Software
NameVersionClassification
HKL-3000data scaling
REFMAC5.8.0131refinement
PDB_EXTRACT3.15data extraction
MOLREPphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UR4

3ur4


Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.921 / WRfactor Rfree: 0.2279 / WRfactor Rwork: 0.1967 / FOM work R set: 0.8502 / SU B: 3.178 / SU ML: 0.1 / SU R Cruickshank DPI: 0.1554 / SU Rfree: 0.1364 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.155 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2279 1042 2.1 %RANDOM
Rwork0.1967 ---
obs0.1973 48908 96.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 54.25 Å2 / Biso mean: 20.624 Å2 / Biso min: 10.79 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å20.8 Å2-0.05 Å2
2--1.27 Å20.4 Å2
3----1.59 Å2
Refinement stepCycle: final / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4676 0 128 331 5135
Biso mean--25.1 29.2 -
Num. residues----608
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195008
X-RAY DIFFRACTIONr_angle_refined_deg1.4171.9316816
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4315635
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.10725.161186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.14315830
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.85157
X-RAY DIFFRACTIONr_chiral_restr0.090.2758
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213917
X-RAY DIFFRACTIONr_mcbond_it0.8961.9522500
X-RAY DIFFRACTIONr_mcangle_it1.3872.9233141
X-RAY DIFFRACTIONr_scbond_it1.1282.062508
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 67 -
Rwork0.238 3136 -
all-3203 -
obs--84.36 %

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