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(-) Description

Title :  IDENTIFICATION OF A NOVEL PPARG LIGAND THAT REGULATES METABOLISM
 
Authors :  R. Wang, Y. Li
Date :  09 Feb 15  (Deposition) - 09 Sep 15  (Release) - 09 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.98
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Af-2 Helix, Ligand Binding Pocket, Three-Layer Helical Sandwich, Transcription Regulator Pparg, Nr1C3, Peroxisome Proliferator- Activated Receptor Gamma, Nhr, Nuclear Receptor, Coactivator, Transcription Factor, Dna Binding Protein-Transcription Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. L. Zheng, L. Qiu, R. Wang, X. H. Feng, Y. P. Han, Y. L. Zhu, D. Z. Chen, Y. J. Liu, L. H. Jin, Y. Li
Selective Targeting Of Ppar Gamma By The Natural Product Chelerythrine With A Unique Binding Mode And Improved Antidiabetic Potency.
Sci Rep V. 5 12222 2015
PubMed-ID: 26183621  |  Reference-DOI: 10.1038/SREP12222

(-) Compounds

Molecule 1 - PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR GAMMA
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET24
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 236-504
    Gene: PPARG, NR1C3
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PPAR-GAMMA,NUCLEAR RECEPTOR SUBFAMILY 1 GROUP C MEMBER 3
 
Molecule 2 - PEPTIDE FROM NUCLEAR RECEPTOR COACTIVATOR 1
    Chains: B
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: NCOA-1,CLASS E BASIC HELIX-LOOP-HELIX PROTEIN 74,BHLHE74, PROTEIN HIN-2,RIP160,RENAL CARCINOMA ANTIGEN NY-REN-52,STEROID RECEPTOR COACTIVATOR 1,SRC-1
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1CTI1Ligand/Ion1,2-DIMETHOXY-12-METHYL[1,3]BENZODIOXOLO[5,6-C]PHENANTHRIDIN-12-IUM

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:281 , CYS A:285 , ARG A:288 , SER A:289 , LEU A:330 , LEU A:333 , LEU A:340 , LEU A:353 , PHE A:360 , MET A:364 , HOH A:742binding site for residue CTI A 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Y29)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Lys A:244 -Ser A:245
2Lys A:261 -Ile A:262
3Lys A:358 -Pro A:359

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Y29)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Y29)

(-) Exons   (0, 0)

(no "Exon" information available for 4Y29)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:257
                                                                                                                                                                                                                                                                                                  
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh.......eee.hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhee..eeee....eeeehhhhhh...hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4y29 A  208 SADLRALAKHLYDSYIKSFPLTKAKARAILTGKTTDKSPFVIYDMNSLMMGEDKIKEVAIRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQEIYKDL  476
                                   217       227       237       247       257    || 279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       
                                                                                262|                                                                                                                                                                                                         
                                                                                 275                                                                                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:10
                                           
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                4y29 B 1432 KSLLQQLLTE 1441
                                  1441
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4Y29)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Y29)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Y29)

(-) Gene Ontology  (148, 165)

Asymmetric/Biological Unit(hide GO term definitions)

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    Lys A:261 - Ile A:262   [ RasMol ]  
    Lys A:358 - Pro A:359   [ RasMol ]  
 

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  4y29
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  NCOA1_HUMAN | Q15788
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  PPARG_HUMAN | P37231
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        NCOA1_HUMAN | Q15788: 1fm6 1fm9 1k4w 1k74 1k7l 1kv6 1n4h 1nq7 1nrl 1p8d 1pzl 1rdt 1tfc 1u3r 1u3s 1x76 1x78 1x7b 1x7j 1xiu 1xv9 1xvp 1yy4 1yye 1zaf 2a3i 2c52 2fvj 2gtk 2hbh 2hc4 2hcd 2hfp 2npa 2nv7 2p54 2prg 3bej 3bqd 3ctb 3cwd 3dct 3dcu 3dr1 3et1 3et3 3fei 3fej 3fur 3fxv 3g8i 3g9e 3gyt 3gyu 3h0a 3hc5 3hc6 3hvl 3ipq 3ips 3ipu 3kmr 3lmp 3okh 3oki 3olf 3oll 3ols 3omk 3omm 3omo 3omp 3omq 3oof 3ook 3p88 3p89 3qt0 3rut 3ruu 3rvf 3s9s 3t03 3uu7 3uua 3uud 3v9y 3vn2 4dk7 4dk8 4dm6 4dm8 4dqm 4f9m 4fgy 4g1d 4g1y 4g1z 4g20 4g21 4g2h 4hee 4j5w 4j5x 4jyg 4jyh 4jyi 4mg5 4mg6 4mg7 4mg8 4mg9 4mga 4mgb 4mgc 4mgd 4ruj 4rup 4tuz 4tv1 4uda 4udb 5a86 5avi 5avl 5azt 5dsh 5dv3 5dv6 5dv8 5dvc 5dwl 5e7v 5hjs 5ji0 5jmm 5l7e 5l7g 5l7h 5nma 5x8u 5x8w
        PPARG_HUMAN | P37231: 1fm6 1fm9 1i7i 1k74 1knu 1nyx 1prg 1rdt 1wm0 1zeo 1zgy 2ath 2f4b 2fvj 2g0g 2g0h 2gtk 2hfp 2hwq 2hwr 2i4j 2i4p 2i4z 2om9 2p4y 2pob 2prg 2q59 2q5p 2q5s 2q61 2q6r 2q6s 2q8s 2qmv 2vsr 2vst 2vv0 2vv1 2vv2 2vv3 2vv4 2xkw 2yfe 2zk0 2zk1 2zk2 2zk3 2zk4 2zk5 2zk6 2zno 2zvt 3ads 3adt 3adu 3adv 3adw 3adx 3an3 3an4 3b0q 3b0r 3b1m 3b3k 3bc5 3cdp 3cds 3cs8 3cwd 3d6d 3dzu 3dzy 3e00 3et0 3et3 3fej 3fur 3g9e 3gbk 3h0a 3ho0 3hod 3ia6 3k8s 3kmg 3lmp 3noa 3osi 3osw 3pba 3po9 3prg 3qt0 3r5n 3r8a 3r8i 3s9s 3sz1 3t03 3ty0 3u9q 3v9t 3v9v 3v9y 3vjh 3vji 3vn2 3vso 3vsp 3wj4 3wj5 3wmh 3x1h 3x1i 4a4v 4a4w 4ci5 4e4k 4e4q 4em9 4ema 4f9m 4fgy 4hee 4jaz 4jl4 4l96 4l98 4o8f 4oj4 4prg 4pvu 4pwl 4r06 4r2u 4r6s 4xld 4xta 4xuh 4xum 4yt1 5azv 5dsh 5dv3 5dv6 5dv8 5dvc 5dwl 5f9b 5gtn 5gto 5gtp 5hzc 5ji0 5tto 5two

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4Y29)