Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF PPARGAMMMA IN COMPLEX WITH SR1663
 
Authors :  D. P. Marciano, P. R. Griffin, J. B. Bruning
Date :  26 Aug 14  (Deposition) - 01 Jul 15  (Release) - 01 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A (1x),B (1x)
Keywords :  Nuclear Receptor Ligand Binding Domain, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. P. Marciano, D. S. Kuruvilla, S. V. Boregowda, A. Asteian, T. S. Hughes, R. Garcia-Ordonez, C. A. Corzo, T. M. Khan, S. J. Novick, H. Park, D. J. Kojetin, D. G. Phinney, J. B. Bruning, T. M. Kamenecka, P. R. Griffin
Pharmacological Repression Of Ppar Gamma Promotes Osteogenesis.
Nat Commun V. 6 7443 2015
PubMed-ID: 26068133  |  Reference-DOI: 10.1038/NCOMMS8443

(-) Compounds

Molecule 1 - PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR GAMMA
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG19
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 231-505
    Gene: NR1C3, PPARG
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PPAR-GAMMA, NUCLEAR RECEPTOR SUBFAMILY 1 GROUP C MEMBER 3

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (1x): A (1x)B (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
13K22Ligand/Ion4'-[(2,3-DIMETHYL-5-{[(1R)-1-(4-NITROPHENYL)ETHYL]CARBAMOYL}-1H-INDOL-1-YL)METHYL]BIPHENYL-2-CARBOXYLIC ACID
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
13K22Ligand/Ion4'-[(2,3-DIMETHYL-5-{[(1R)-1-(4-NITROPHENYL)ETHYL]CARBAMOYL}-1H-INDOL-1-YL)METHYL]BIPHENYL-2-CARBOXYLIC ACID
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
13K21Ligand/Ion4'-[(2,3-DIMETHYL-5-{[(1R)-1-(4-NITROPHENYL)ETHYL]CARBAMOYL}-1H-INDOL-1-YL)METHYL]BIPHENYL-2-CARBOXYLIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:281 , PHE A:282 , CYS A:285 , GLN A:286 , ARG A:288 , SER A:289 , TYR A:327 , LEU A:330 , ILE A:341 , SER A:342 , HIS A:449 , LEU A:453 , TYR A:473BINDING SITE FOR RESIDUE 3K2 A 501
2AC2SOFTWAREPHE B:282 , CYS B:285 , GLN B:286 , ARG B:288 , SER B:289 , HIS B:323 , ILE B:326 , TYR B:327 , LEU B:330 , ILE B:341 , SER B:342 , LYS B:367 , HIS B:449 , LEU B:453BINDING SITE FOR RESIDUE 3K2 B 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4R6S)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Lys A:358 -Pro A:359
2Lys B:358 -Pro B:359

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4R6S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4R6S)

(-) Exons   (0, 0)

(no "Exon" information available for 4R6S)

(-) Sequences/Alignments

Asymmetric 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:262
                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh........eee.hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhee..eeeehhh.eeeehhhhhh...hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r6s A 203 QLNPESADLRALAKHLYDSYIKSFPLTKAKARAILTGKTTDKSPFVIYDMNSLMMGEDKIKEVAIRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVFEHVQLLQVIKKTETDMSLHPLLQEIYKDL 476
                                   212       222       232       242       252       262||     284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474  
                                                                                      263|                                                                                                                                                                                                        
                                                                                       276                                                                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:254
                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh....eee.hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh.ee..eeeehhh.eeeehhhhhh...hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r6s B 207 ESADLRALAKHLYDSYIKSFPLTKAKARAILTGKKSPFVIYDMNSLMMGEDKIKFKHIKEVAIRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVFEHVQLLQVIKKTETHPLLQEIYK 474
                                   216       226       236   ||  249       259       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456    || 470    
                                                           240|                    267|                                                                                                                                                                                       461|        
                                                            244                     275                                                                                                                                                                                        466
   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 4R6S)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4R6S)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4R6S)

(-) Gene Ontology  (107, 107)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    3K2  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Lys A:358 - Pro A:359   [ RasMol ]  
    Lys B:358 - Pro B:359   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4r6s
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PPARG_HUMAN | P37231
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  PPARG_HUMAN | P37231
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        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 4xld 4xta 4xuh 4xum 4y29 4yt1 5azv 5dsh 5dv3 5dv6 5dv8 5dvc 5dwl 5f9b 5gtn 5gto 5gtp 5hzc 5ji0 5tto 5two

(-) Related Entries Specified in the PDB File

4r2u CRYSTAL STRUCTURE OF PPARGAMMA IN COMPLEX WITH SR1664