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- PDB-7dno: Characterization of Peptide Ligands Against WDR5 Isolated Using P... -

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Basic information

Entry
Database: PDB / ID: 7dno
TitleCharacterization of Peptide Ligands Against WDR5 Isolated Using Phage Display Technique
Components
  • CYS-ARG-THR-LEU-PRO-PHE
  • WD repeat-containing protein 5
KeywordsPEPTIDE BINDING PROTEIN / inhibitor
Function / homology
Function and homology information


MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / Cardiogenesis / regulation of tubulin deacetylation / histone methyltransferase complex / 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 / regulation of tubulin deacetylation / histone methyltransferase complex / 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
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
Similarity search - Domain/homology
WD repeat-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsCao, J. / Cao, D. / Xiong, B. / Li, Y. / Fan, T.
CitationJournal: Molecules / Year: 2021
Title: Phage-Display Based Discovery and Characterization of Peptide Ligands against WDR5.
Authors: Cao, J. / Fan, T. / Li, Y. / Du, Z. / Chen, L. / Wang, Y. / Wang, X. / Shen, J. / Huang, X. / Xiong, B. / Cao, D.
History
DepositionDec 10, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: Database references / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / database_2
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: CYS-ARG-THR-LEU-PRO-PHE
D: CYS-ARG-THR-LEU-PRO-PHE


Theoretical massNumber of molelcules
Total (without water)71,0574
Polymers71,0574
Non-polymers00
Water5,513306
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-10 kcal/mol
Surface area22950 Å2
Unit cell
Length a, b, c (Å)46.735, 53.912, 64.788
Angle α, β, γ (deg.)69.817, 88.790, 74.163
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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


Mass: 34421.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR5, BIG3 / Plasmid: PET28 / Production host: Homo sapiens (human) / References: UniProt: P61964
#2: Protein/peptide CYS-ARG-THR-LEU-PRO-PHE


Mass: 1107.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 2.07 Å3/Da / Density % sol: 40.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M BisTris pH 6.0, 0.2M ammonium acetate, 20-30% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97919 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 15, 2020 / Details: x-ray
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 2.03→30.31 Å / Num. obs: 32798 / % possible obs: 88.98 % / Redundancy: 3.3 % / Biso Wilson estimate: 28.11 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.072 / Net I/σ(I): 12.16
Reflection shellResolution: 2.03→2.14 Å / Num. unique obs: 3122 / CC1/2: 0.846 / CC star: 0.957

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UVL

3uvl


Resolution: 2.03→30.31 Å / SU ML: 0.2558 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 27.5464
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2268 1621 4.94 %
Rwork0.1793 31177 -
obs0.1817 32798 88.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.8 Å2
Refinement stepCycle: LAST / Resolution: 2.03→30.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4786 0 0 306 5092
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00784898
X-RAY DIFFRACTIONf_angle_d1.05566642
X-RAY DIFFRACTIONf_chiral_restr0.0615754
X-RAY DIFFRACTIONf_plane_restr0.0094820
X-RAY DIFFRACTIONf_dihedral_angle_d12.7701640
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.090.3222690.2881333X-RAY DIFFRACTION46.06
2.09-2.150.34441100.25942256X-RAY DIFFRACTION76.92
2.15-2.230.30051310.24422743X-RAY DIFFRACTION92.65
2.23-2.320.31251050.23652030X-RAY DIFFRACTION69.61
2.32-2.430.25681680.22372785X-RAY DIFFRACTION96.06
2.43-2.550.26321550.22142836X-RAY DIFFRACTION96.33
2.55-2.710.2761440.19992832X-RAY DIFFRACTION97.89
2.71-2.920.25241620.19312886X-RAY DIFFRACTION98.23
2.92-3.220.22141520.18172859X-RAY DIFFRACTION98.01
3.22-3.680.20161490.15352869X-RAY DIFFRACTION98.56
3.68-4.630.18741540.13992904X-RAY DIFFRACTION98.45
4.63-30.310.18011220.15542844X-RAY DIFFRACTION96.52

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