Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3SMR

Crystal structure of human WD repeat domain 5 with compound

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000122	biological_process	negative regulation of transcription by RNA polymerase II
A	0000123	cellular_component	histone acetyltransferase complex
A	0001501	biological_process	skeletal system development
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0005654	cellular_component	nucleoplasm
A	0005669	cellular_component	transcription factor TFIID complex
A	0006094	biological_process	gluconeogenesis
A	0006325	biological_process	chromatin organization
A	0006355	biological_process	regulation of DNA-templated transcription
A	0006357	biological_process	regulation of transcription by RNA polymerase II
A	0006367	biological_process	transcription initiation at RNA polymerase II promoter
A	0016251	molecular_function	RNA polymerase II general transcription initiation factor activity
A	0035064	molecular_function	methylated histone binding
A	0035097	cellular_component	histone methyltransferase complex
A	0042393	molecular_function	histone binding
A	0042800	molecular_function	histone H3K4 methyltransferase activity
A	0044545	cellular_component	NSL complex
A	0044665	cellular_component	MLL1/2 complex
A	0044666	cellular_component	MLL3/4 complex
A	0045722	biological_process	positive regulation of gluconeogenesis
A	0045815	biological_process	transcription initiation-coupled chromatin remodeling
A	0045893	biological_process	positive regulation of DNA-templated transcription
A	0045995	biological_process	regulation of embryonic development
A	0048188	cellular_component	Set1C/COMPASS complex
A	0051302	biological_process	regulation of cell division
A	0051726	biological_process	regulation of cell cycle
A	0071339	cellular_component	MLL1 complex
A	0072686	cellular_component	mitotic spindle
A	0090043	biological_process	regulation of tubulin deacetylation
A	0140672	cellular_component	ATAC complex
B	0000122	biological_process	negative regulation of transcription by RNA polymerase II
B	0000123	cellular_component	histone acetyltransferase complex
B	0001501	biological_process	skeletal system development
B	0005515	molecular_function	protein binding
B	0005634	cellular_component	nucleus
B	0005654	cellular_component	nucleoplasm
B	0005669	cellular_component	transcription factor TFIID complex
B	0006094	biological_process	gluconeogenesis
B	0006325	biological_process	chromatin organization
B	0006355	biological_process	regulation of DNA-templated transcription
B	0006357	biological_process	regulation of transcription by RNA polymerase II
B	0006367	biological_process	transcription initiation at RNA polymerase II promoter
B	0016251	molecular_function	RNA polymerase II general transcription initiation factor activity
B	0035064	molecular_function	methylated histone binding
B	0035097	cellular_component	histone methyltransferase complex
B	0042393	molecular_function	histone binding
B	0042800	molecular_function	histone H3K4 methyltransferase activity
B	0044545	cellular_component	NSL complex
B	0044665	cellular_component	MLL1/2 complex
B	0044666	cellular_component	MLL3/4 complex
B	0045722	biological_process	positive regulation of gluconeogenesis
B	0045815	biological_process	transcription initiation-coupled chromatin remodeling
B	0045893	biological_process	positive regulation of DNA-templated transcription
B	0045995	biological_process	regulation of embryonic development
B	0048188	cellular_component	Set1C/COMPASS complex
B	0051302	biological_process	regulation of cell division
B	0051726	biological_process	regulation of cell cycle
B	0071339	cellular_component	MLL1 complex
B	0072686	cellular_component	mitotic spindle
B	0090043	biological_process	regulation of tubulin deacetylation
B	0140672	cellular_component	ATAC complex
C	0000122	biological_process	negative regulation of transcription by RNA polymerase II
C	0000123	cellular_component	histone acetyltransferase complex
C	0001501	biological_process	skeletal system development
C	0005515	molecular_function	protein binding
C	0005634	cellular_component	nucleus
C	0005654	cellular_component	nucleoplasm
C	0005669	cellular_component	transcription factor TFIID complex
C	0006094	biological_process	gluconeogenesis
C	0006325	biological_process	chromatin organization
C	0006355	biological_process	regulation of DNA-templated transcription
C	0006357	biological_process	regulation of transcription by RNA polymerase II
C	0006367	biological_process	transcription initiation at RNA polymerase II promoter
C	0016251	molecular_function	RNA polymerase II general transcription initiation factor activity
C	0035064	molecular_function	methylated histone binding
C	0035097	cellular_component	histone methyltransferase complex
C	0042393	molecular_function	histone binding
C	0042800	molecular_function	histone H3K4 methyltransferase activity
C	0044545	cellular_component	NSL complex
C	0044665	cellular_component	MLL1/2 complex
C	0044666	cellular_component	MLL3/4 complex
C	0045722	biological_process	positive regulation of gluconeogenesis
C	0045815	biological_process	transcription initiation-coupled chromatin remodeling
C	0045893	biological_process	positive regulation of DNA-templated transcription
C	0045995	biological_process	regulation of embryonic development
C	0048188	cellular_component	Set1C/COMPASS complex
C	0051302	biological_process	regulation of cell division
C	0051726	biological_process	regulation of cell cycle
C	0071339	cellular_component	MLL1 complex
C	0072686	cellular_component	mitotic spindle
C	0090043	biological_process	regulation of tubulin deacetylation
C	0140672	cellular_component	ATAC complex
D	0000122	biological_process	negative regulation of transcription by RNA polymerase II
D	0000123	cellular_component	histone acetyltransferase complex
D	0001501	biological_process	skeletal system development
D	0005515	molecular_function	protein binding
D	0005634	cellular_component	nucleus
D	0005654	cellular_component	nucleoplasm
D	0005669	cellular_component	transcription factor TFIID complex
D	0006094	biological_process	gluconeogenesis
D	0006325	biological_process	chromatin organization
D	0006355	biological_process	regulation of DNA-templated transcription
D	0006357	biological_process	regulation of transcription by RNA polymerase II
D	0006367	biological_process	transcription initiation at RNA polymerase II promoter
D	0016251	molecular_function	RNA polymerase II general transcription initiation factor activity
D	0035064	molecular_function	methylated histone binding
D	0035097	cellular_component	histone methyltransferase complex
D	0042393	molecular_function	histone binding
D	0042800	molecular_function	histone H3K4 methyltransferase activity
D	0044545	cellular_component	NSL complex
D	0044665	cellular_component	MLL1/2 complex
D	0044666	cellular_component	MLL3/4 complex
D	0045722	biological_process	positive regulation of gluconeogenesis
D	0045815	biological_process	transcription initiation-coupled chromatin remodeling
D	0045893	biological_process	positive regulation of DNA-templated transcription
D	0045995	biological_process	regulation of embryonic development
D	0048188	cellular_component	Set1C/COMPASS complex
D	0051302	biological_process	regulation of cell division
D	0051726	biological_process	regulation of cell cycle
D	0071339	cellular_component	MLL1 complex
D	0072686	cellular_component	mitotic spindle
D	0090043	biological_process	regulation of tubulin deacetylation
D	0140672	cellular_component	ATAC complex

Functional Information from PDB Data

site_id	AC1
Number of Residues	12
Details	BINDING SITE FOR RESIDUE NP7 A 1000

Chain	Residue
A	SER49
A	CYS261
A	HOH576
A	HOH647
A	SER50
A	ILE90
A	SER91
A	ASP92
A	PHE133
A	PRO173
A	SER175
A	TYR191

site_id	AC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO A 2002

Chain	Residue
A	PRO55
A	TRP95
A	SER96
A	SER97
A	PHE137
A	EDO2003

site_id	AC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO A 2003

Chain	Residue
A	ASN136
A	HIS178
A	LYS221
A	HOH522
A	HOH616
A	EDO2002

site_id	AC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO A 2004

Chain	Residue
A	LEU164
A	LYS165
A	THR200
A	ALA201

site_id	AC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO A 2013

Chain	Residue
A	LYS165
A	ALA201
A	SER202
B	HIS44
B	HOH560

site_id	AC6
Number of Residues	2
Details	BINDING SITE FOR RESIDUE EDO A 2014

Chain	Residue
A	TRP241
A	HOH581

site_id	AC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO A 2015

Chain	Residue
A	TYR260
A	ASP302
A	LEU321
A	GLU322

site_id	AC8
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO A 2018

Chain	Residue
A	ASP199
A	SER202
A	LEU206
B	THR301
B	ASP324
B	THR326
B	LYS328

site_id	AC9
Number of Residues	2
Details	BINDING SITE FOR RESIDUE EDO A 2020

Chain	Residue
A	LYS250
A	GLN289

site_id	BC1
Number of Residues	15
Details	BINDING SITE FOR RESIDUE NP7 B 1000

Chain	Residue
B	SER49
B	SER50
B	ILE90
B	SER91
B	ASP92
B	ASP107
B	PHE133
B	SER175
B	TYR191
B	CYS261
B	ILE305
B	HOH517
B	HOH540
B	HOH611
B	HOH692

site_id	BC2
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO B 2000

Chain	Residue
B	TYR228
B	LYS250
B	GLN289

site_id	BC3
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO B 2001

Chain	Residue
B	ASP98
B	ASN100
C	LYS38

site_id	BC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO B 2005

Chain	Residue
B	TRP95
B	SER97
B	PHE137
B	ASN138
B	EDO2022

site_id	BC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO B 2006

Chain	Residue
B	LYS165
B	THR200
B	ALA201

site_id	BC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO B 2007

Chain	Residue
B	VAL31
B	GLY271
B	LYS272
B	TRP273
B	ASN287

site_id	BC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO B 2022

Chain	Residue
B	SER97
B	HOH593
B	EDO2005
C	ASP76

site_id	BC8
Number of Residues	12
Details	BINDING SITE FOR RESIDUE NP7 C 1000

Chain	Residue
C	SER49
C	SER50
C	ILE90
C	SER91
C	ASP92
C	PHE133
C	PRO173
C	SER175
C	TYR191
C	CYS261
C	ILE305
C	HOH660

site_id	BC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO C 2008

Chain	Residue
C	GLY271
C	LYS272
C	ASN287
C	VAL31

site_id	CC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO C 2009

Chain	Residue
C	TYR260
C	ASP302
C	GLU322

site_id	CC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO C 2010

Chain	Residue
C	THR40
C	THR301
C	ASP324
C	THR326
C	LYS328
D	LEU206

site_id	CC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO C 2017

Chain	Residue
C	PHE39
C	ALA74
C	TYR75
C	LEU329

site_id	CC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO C 2021

Chain	Residue
C	TYR228
C	LYS250
C	GLN289
C	HOH595

site_id	CC5
Number of Residues	13
Details	BINDING SITE FOR RESIDUE NP7 D 1000

Chain	Residue
D	SER49
D	SER50
D	ILE90
D	SER91
D	ASP92
D	PHE133
D	SER175
D	TYR191
D	CYS261
D	ILE305
D	HOH596
D	HOH636
D	HOH680

site_id	CC6
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO D 2011

Chain	Residue
D	LYS165
D	THR200
D	ALA201

site_id	CC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO D 2012

Chain	Residue
D	TYR228
D	LYS250
D	GLN289
D	HOH602

site_id	CC8
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO D 2016

Chain	Residue
D	PHE39
D	ALA74
D	TYR75
D	ILE315
D	LEU329

site_id	CC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO D 2019

Chain	Residue
C	LEU206
D	THR40
D	THR301
D	ASP324
D	THR326
D	LYS328

Functional Information from PROSITE/UniProt

site_id	PS00678
Number of Residues	15
Details	WD_REPEATS_1 Trp-Asp (WD) repeats signature. LVSAsdDkTLKIWDV

Chain	Residue	Details
A	LEU102-VAL116
A	ILE144-VAL158
A	ILE186-THR200
A	ILE274-LEU288

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	16
Details	SITE: Important for interaction with histone H3

Chain	Residue	Details
A	ASP107
C	PHE133
C	PHE263
C	GLU322
D	ASP107
D	PHE133
D	PHE263
D	GLU322
A	PHE133
A	PHE263
A	GLU322
B	ASP107
B	PHE133
B	PHE263
B	GLU322
C	ASP107

site_id	SWS_FT_FI2
Number of Residues	4
Details	MOD_RES: N6-acetyllysine => ECO:0007744\|PubMed:19608861

Chain	Residue	Details
A	LYS112
B	LYS112
C	LYS112
D	LYS112

site_id	SWS_FT_FI3
Number of Residues	12
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744\|PubMed:28112733

Chain	Residue	Details
A	LYS27
D	LYS27
D	LYS46
A	LYS46
B	LYS27
B	LYS46
C	LYS27
C	LYS46

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)