Structure of PDB 6zrd Chain B

Receptor sequence

>6zrdB (length=389) Species: 9606 (Homo sapiens) [Search protein sequence]

MADKEAAFDDAVEERVINEEYKIWKKNTPFLYDLVMTHALEWPSLTAQWL
PDVTRPEGKDFSIHRLVLGTHTSDEQNHLVIASVQLPNDDGKIEIEIKIN
HEGEVNRARYMPQNPCIIATKTPSSDVLVFDYTKHPSKPDPSGECNPDLR
LRGHQKEGYGLSWNPNLSGHLLSASDDHTICLWDISAVPKEGKVVDAKTI
FTGHTAVVEDVSWHLLHESLFGSVADDQKLMIWDTRSNNTSKPSHSVDAH
TAEVNCLSFNPYSEFILATGSADKTVALWDLRNLKLKLHSFESHKDEIFQ
VQWSPHNETILASSGTDRRLNVWDLSKIGEEQSPEDAEDGPPELLFIHGG
HTAKISDFSWNPNEPWVICSVSEDNIMQVWQMAENIYND

3D structure

PDB

6zrd Structure Based Design of Bicyclic Peptide Inhibitors of RbAp48.

Chain

Resolution

2.5 Å

3D
structure

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Enzymatic activity

Enzyme Commision number

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	peptide	B	E20 I23 N27 F30 L31 R341 D358 D361 G362 P363 F368 I369 G371 N407 I408 D411	E20 I23 N27 F30 L31 R319 D336 D339 G340 P341 F346 I347 G349 N385 I386 D389

Gene Ontology

	Molecular Function
GO:0000978	RNA polymerase II cis-regulatory region sequence-specific DNA binding
GO:0005515	protein binding
GO:0008094	ATP-dependent activity, acting on DNA
GO:0031492	nucleosomal DNA binding
GO:0042393	histone binding
GO:0042826	histone deacetylase binding

	Biological Process
GO:0000122	negative regulation of transcription by RNA polymerase II
GO:0006260	DNA replication
GO:0006325	chromatin organization
GO:0006334	nucleosome assembly
GO:0006335	DNA replication-dependent chromatin assembly
GO:0006338	chromatin remodeling
GO:0006355	regulation of DNA-templated transcription
GO:0007420	brain development
GO:0008285	negative regulation of cell population proliferation
GO:0030336	negative regulation of cell migration
GO:0030512	negative regulation of transforming growth factor beta receptor signaling pathway
GO:0042659	regulation of cell fate specification
GO:0045892	negative regulation of DNA-templated transcription
GO:0045893	positive regulation of DNA-templated transcription
GO:1902455	negative regulation of stem cell population maintenance
GO:1902459	positive regulation of stem cell population maintenance
GO:2000736	regulation of stem cell differentiation

	Cellular Component
GO:0000118	histone deacetylase complex
GO:0000781	chromosome, telomeric region
GO:0000785	chromatin
GO:0005634	nucleus
GO:0005654	nucleoplasm
GO:0005694	chromosome
GO:0005829	cytosol
GO:0016581	NuRD complex
GO:0016589	NURF complex
GO:0032991	protein-containing complex
GO:0033186	CAF-1 complex
GO:0035098	ESC/E(Z) complex
GO:0070822	Sin3-type complex
GO:1904949	ATPase complex

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Molecular Function

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Biological Process

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Cellular Component

External links

PDB	RCSB:6zrd, PDBe:6zrd, PDBj:6zrd
PDBsum	6zrd
PubMed	33022847
UniProt	Q09028\|RBBP4_HUMAN Histone-binding protein RBBP4 (Gene Name=RBBP4)

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