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- PDB-6pgd: WDR5delta32 bound to peptidomimetic -

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Basic information

Entry
Database: PDB / ID: 6pgd
TitleWDR5delta32 bound to peptidomimetic
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


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
Chem-OK4 / WD repeat-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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)34,2505
Polymers33,5371
Non-polymers7134
Water7,728429
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area480 Å2
ΔGint-33 kcal/mol
Surface area11760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.698, 65.240, 97.195
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-OK4 / N-acetyl-L-alanyl-5-[5-(hydroxymethyl)-1H-imidazol-2-yl]-L-norvalyl-L-valinamide


Type: peptide-like / Mass: 424.495 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H32N6O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 429 / 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: 44.28 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop
Details: 0.233 M ammonium sulfate, 0.1 M Bis-Tris chloride, pH 6.02, 26% w/v PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 22, 2016
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.5→46.7 Å / Num. obs: 47878 / % possible obs: 99 % / Redundancy: 7.2 % / CC1/2: 0.997 / Net I/σ(I): 11
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1846 / CC1/2: 0.742 / % possible all: 80.5

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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: 1.5→35.39 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.962 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.065 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16718 2353 4.9 %RANDOM
Rwork0.1507 ---
obs0.15153 45458 99.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 10.419 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å2-0 Å2
2---0.14 Å2-0 Å2
3---0.04 Å2
Refinement stepCycle: 1 / Resolution: 1.5→35.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2360 0 45 429 2834
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132556
X-RAY DIFFRACTIONr_bond_other_d0.0360.0172341
X-RAY DIFFRACTIONr_angle_refined_deg1.4081.6413477
X-RAY DIFFRACTIONr_angle_other_deg2.3231.6055474
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3755323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.11624.369103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.32715444
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.145155
X-RAY DIFFRACTIONr_chiral_restr0.0720.2335
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022851
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02513
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_it0.6420.9181268
X-RAY DIFFRACTIONr_mcbond_other0.6410.9171267
X-RAY DIFFRACTIONr_mcangle_it1.0821.3741599
X-RAY DIFFRACTIONr_mcangle_other1.0821.3751600
X-RAY DIFFRACTIONr_scbond_it1.1111.0491288
X-RAY DIFFRACTIONr_scbond_other1.0931.0361277
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7321.51861
X-RAY DIFFRACTIONr_long_range_B_refined4.29412.5332921
X-RAY DIFFRACTIONr_long_range_B_other4.29412.5322922
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 151 -
Rwork0.226 2896 -
obs--87.01 %

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