3DZU

Intact PPAR gamma - RXR alpha Nuclear Receptor Complex on DNA bound with BVT.13, 9-cis Retinoic Acid and NCOA2 Peptide

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000122	biological_process	negative regulation of transcription by RNA polymerase II
A	0000785	cellular_component	chromatin
A	0000976	molecular_function	transcription cis-regulatory region binding
A	0000977	molecular_function	RNA polymerase II transcription regulatory region sequence-specific DNA binding
A	0000978	molecular_function	RNA polymerase II cis-regulatory region sequence-specific DNA binding
A	0000981	molecular_function	DNA-binding transcription factor activity, RNA polymerase II-specific
A	0001221	molecular_function	transcription coregulator binding
A	0001972	molecular_function	retinoic acid binding
A	0002157	biological_process	positive regulation of thyroid hormone receptor signaling pathway
A	0003677	molecular_function	DNA binding
A	0003690	molecular_function	double-stranded DNA binding
A	0003700	molecular_function	DNA-binding transcription factor activity
A	0003707	molecular_function	nuclear steroid receptor activity
A	0004879	molecular_function	nuclear receptor activity
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0005654	cellular_component	nucleoplasm
A	0005667	cellular_component	transcription regulator complex
A	0005737	cellular_component	cytoplasm
A	0005739	cellular_component	mitochondrion
A	0005829	cellular_component	cytosol
A	0006355	biological_process	regulation of DNA-templated transcription
A	0007399	biological_process	nervous system development
A	0008270	molecular_function	zinc ion binding
A	0009755	biological_process	hormone-mediated signaling pathway
A	0010875	biological_process	positive regulation of cholesterol efflux
A	0019899	molecular_function	enzyme binding
A	0030154	biological_process	cell differentiation
A	0030224	biological_process	monocyte differentiation
A	0030501	biological_process	positive regulation of bone mineralization
A	0030518	biological_process	nuclear receptor-mediated steroid hormone signaling pathway
A	0032526	biological_process	response to retinoic acid
A	0035357	biological_process	peroxisome proliferator activated receptor signaling pathway
A	0042277	molecular_function	peptide binding
A	0042789	biological_process	mRNA transcription by RNA polymerase II
A	0042802	molecular_function	identical protein binding
A	0042809	molecular_function	nuclear vitamin D receptor binding
A	0043235	cellular_component	receptor complex
A	0043565	molecular_function	sequence-specific DNA binding
A	0044323	molecular_function	retinoic acid-responsive element binding
A	0045834	biological_process	positive regulation of lipid metabolic process
A	0045893	biological_process	positive regulation of DNA-templated transcription
A	0045944	biological_process	positive regulation of transcription by RNA polymerase II
A	0046872	molecular_function	metal ion binding
A	0048384	biological_process	retinoic acid receptor signaling pathway
A	0048469	biological_process	cell maturation
A	0050692	molecular_function	DNA binding domain binding
A	0050693	molecular_function	LBD domain binding
A	0070564	biological_process	positive regulation of vitamin D receptor signaling pathway
A	0070644	molecular_function	vitamin D response element binding
A	0071404	biological_process	cellular response to low-density lipoprotein particle stimulus
A	0071630	biological_process	nuclear protein quality control by the ubiquitin-proteasome system
A	0090575	cellular_component	RNA polymerase II transcription regulator complex
A	0140077	biological_process	positive regulation of lipoprotein transport
A	1990837	molecular_function	sequence-specific double-stranded DNA binding
D	0003677	molecular_function	DNA binding
D	0003700	molecular_function	DNA-binding transcription factor activity
D	0004879	molecular_function	nuclear receptor activity
D	0005634	cellular_component	nucleus
D	0006355	biological_process	regulation of DNA-templated transcription
D	0008270	molecular_function	zinc ion binding
D	0043565	molecular_function	sequence-specific DNA binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN D 7121

Chain	Residue
D	CYS111
D	CYS114
D	CYS128
D	CYS131

---

site_id	AC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN D 7122

Chain	Residue
D	CYS148
D	LEU150
D	CYS152
D	CYS162
D	CYS165

---

site_id	AC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN A 7221

Chain	Residue
A	CYS135
A	CYS138
A	CYS152
A	CYS155

---

site_id	AC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN A 7222

Chain	Residue
A	CYS171
A	CYS177
A	CYS187
A	CYS190

---

site_id	AC5
Number of Residues	11
Details	BINDING SITE FOR RESIDUE 9CR A 7223

Chain	Residue
A	ILE268
A	ALA271
A	ALA272
A	GLN275
A	ASN306
A	ILE310
A	PHE313
A	ARG316
A	LEU326
A	CYS432
A	HIS435

---

site_id	AC6
Number of Residues	9
Details	BINDING SITE FOR RESIDUE PLB D 701

Chain	Residue
D	ARG280
D	ILE281
D	GLY284
D	CYS285
D	ARG288
D	LEU333
D	LEU340
D	ILE341
D	SER342

---

Functional Information from PROSITE/UniProt

site_id	PS00031
Number of Residues	27
Details	NUCLEAR_REC_DBD_1 Nuclear hormones receptors DNA-binding region signature. CaiCg.Drssgk.HYgvysCegCkgFFkR

Chain	Residue	Details
A	CYS135-ARG161
D	CYS111-ARG137

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	139
Details	DNA binding: {"description":"Nuclear receptor","evidences":[{"source":"PROSITE-ProRule","id":"PRU00407","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	86
Details	Zinc finger: {"description":"NR C4-type","evidences":[{"source":"PROSITE-ProRule","id":"PRU00407","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	5
Details	Region: {"description":"Nuclear localization signal","evidences":[{"source":"PubMed","id":"12145331","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	20
Details	Region: {"description":"Required for nuclear export","evidences":[{"source":"PubMed","id":"15509776","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	8
Details	Binding site: {"evidences":[{"source":"PubMed","id":"10669605","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1BY4","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	2
Details	Binding site: {"evidences":[{"source":"PubMed","id":"16107141","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"18800767","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19167885","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"2ACL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3FAL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3FC6","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI7
Number of Residues	1
Details	Modified residue: {"description":"N6-acetyllysine; by EP300","evidences":[{"source":"PubMed","id":"17761950","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI8
Number of Residues	75
Details	Region: {"description":"Interaction with FAM120B","evidences":[{"evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI9
Number of Residues	8
Details	Motif: {"description":"9aaTAD","evidences":[{"source":"PubMed","id":"30468856","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI10
Number of Residues	6
Details	Binding site: {"evidences":[{"source":"PubMed","id":"9744270","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"2PRG","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI11
Number of Residues	2
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"36737649","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI12
Number of Residues	8
Details	Motif: {"description":"LXXLL motif 2"}

Chain

Residue

Details

---