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 mediated 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 | 0008270 | molecular_function | zinc ion binding |
| A | 0009755 | biological_process | hormone-mediated signaling pathway |
| A | 0010875 | biological_process | positive regulation of cholesterol efflux |
| A | 0016922 | molecular_function | nuclear receptor binding |
| A | 0019899 | molecular_function | enzyme binding |
| A | 0030154 | biological_process | cell differentiation |
| A | 0030501 | biological_process | positive regulation of bone mineralization |
| A | 0032411 | biological_process | positive regulation of transporter activity |
| 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 | 0043167 | molecular_function | ion binding |
| A | 0043235 | cellular_component | receptor complex |
| A | 0043401 | biological_process | steroid hormone mediated signaling pathway |
| A | 0043565 | molecular_function | sequence-specific DNA binding |
| A | 0044323 | molecular_function | retinoic acid-responsive element binding |
| 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 | 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 | 0090575 | cellular_component | RNA polymerase II transcription regulator complex |
| 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 | 74 |
| Details | DNA_BIND: Nuclear receptor => ECO:0000255|PROSITE-ProRule:PRU00407 |
| Chain | Residue | Details |
| D | ALA108-PHE182 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 42 |
| Details | ZN_FING: NR C4-type => ECO:0000255|PROSITE-ProRule:PRU00407 |
| Chain | Residue | Details |
| D | CYS111-CYS131 | |
| D | CYS148-CYS170 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 4 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:9744270, ECO:0007744|PDB:2PRG |
| Chain | Residue | Details |
| D | GLN286 | |
| D | HIS323 | |
| D | HIS449 | |
| D | TYR473 | |
| A | CYS171 | |
| A | CYS177 | |
| A | CYS187 | |
| A | CYS190 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 1 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| D | SER84 | |
| A | ALA327 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 2 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:36737649 |
| Chain | Residue | Details |
| D | LYS224 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 1 |
| Details | MOD_RES: Phosphoserine => ECO:0000269|PubMed:11162439 |
| Chain | Residue | Details |
| A | SER27 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 3 |
| Details | MOD_RES: Phosphoserine; by MAPK8 and MAPK9 => ECO:0000250|UniProtKB:P28700 |
| Chain | Residue | Details |
| A | SER56 | |
| A | SER70 | |
| A | SER260 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 1 |
| Details | MOD_RES: Phosphothreonine; by MAPK8 and MAPK9 => ECO:0000250|UniProtKB:P28700 |
| Chain | Residue | Details |
| A | THR82 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 1 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| A | SER129 |
| site_id | SWS_FT_FI10 |
| Number of Residues | 1 |
| Details | MOD_RES: N6-acetyllysine; by EP300 => ECO:0000269|PubMed:17761950 |
| Chain | Residue | Details |
| A | LYS145 |
| site_id | SWS_FT_FI11 |
| Number of Residues | 1 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:24275569 |
| Chain | Residue | Details |
| A | SER259 |
| site_id | SWS_FT_FI12 |
| Number of Residues | 2 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO) => ECO:0000269|PubMed:16912044 |
| Chain | Residue | Details |
| A | LYS108 |
