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(-) Description

Title :  HUMAN PPARDELTA LIGAND-BINDING DOMAIN IN COMPLEXED WITH SPECIFIC AGONIST 14
 
Authors :  C. -C. Wu, T. J. Baiga, M. Downes, J. J. La Clair, A. R. Atkins, S. B. Richa T. A. Stockley-Noel, M. E. Bowman, R. M. Evans, J. P. Noel
Date :  03 Dec 16  (Deposition) - 22 Mar 17  (Release) - 05 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Ppardelta, Ligand-Binding Domain, Agonist, Protein Binding-Activator Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. C. Wu, T. J. Baiga, M. Downes, J. J. La Clair, A. R. Atkins, S. B. Richard, W. Fan, T. A. Stockley-Noel, M. E. Bowman, J. P. Noel, R. M. Evans
Structural Basis For Specific Ligation Of The Peroxisome Proliferator-Activated Receptor Delta.
Proc. Natl. Acad. Sci. V. 114 E2563 2017 U. S. A.
PubMed-ID: 28320959  |  Reference-DOI: 10.1073/PNAS.1621513114

(-) Compounds

Molecule 1 - PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR DELTA
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET28A(+)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GenePPARD, NR1C2, PPARB
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsLIGAND-BINDING DOMAIN
    SynonymPPAR-DELTA,NUCI,NUCLEAR HORMONE RECEPTOR 1,NUC1,NUCLEAR RECEPTOR SUBFAMILY 1 GROUP C MEMBER 2,PEROXISOME PROLIFERATOR- ACTIVATED RECEPTOR BETA,PPAR-BETA

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric Unit (4, 11)
No.NameCountTypeFull Name
17SY2Ligand/Ion6-(2-{[CYCLOPROPYL(3'-FLUORO[1,1'-BIPHENYL]-4-CARBONYL)AMINO]METHYL}PHENOXY)HEXANOIC ACID
2B7G3Ligand/IonHEPTYL-BETA-D-GLUCOPYRANOSIDE
3PEG4Ligand/IonDI(HYDROXYETHYL)ETHER
4PGO2Ligand/IonS-1,2-PROPANEDIOL
Biological Unit 1 (4, 4)
No.NameCountTypeFull Name
17SY1Ligand/Ion6-(2-{[CYCLOPROPYL(3'-FLUORO[1,1'-BIPHENYL]-4-CARBONYL)AMINO]METHYL}PHENOXY)HEXANOIC ACID
2B7G1Ligand/IonHEPTYL-BETA-D-GLUCOPYRANOSIDE
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
4PGO1Ligand/IonS-1,2-PROPANEDIOL
Biological Unit 2 (4, 7)
No.NameCountTypeFull Name
17SY1Ligand/Ion6-(2-{[CYCLOPROPYL(3'-FLUORO[1,1'-BIPHENYL]-4-CARBONYL)AMINO]METHYL}PHENOXY)HEXANOIC ACID
2B7G2Ligand/IonHEPTYL-BETA-D-GLUCOPYRANOSIDE
3PEG3Ligand/IonDI(HYDROXYETHYL)ETHER
4PGO1Ligand/IonS-1,2-PROPANEDIOL

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:275 , ASN A:276 , VAL A:279 , THR A:280 , HOH A:664 , HOH A:673 , VAL B:257 , THR B:261 , LYS B:283 , GLU B:435 , ILE B:436 , LYS B:438 , B7G B:501binding site for residue B7G A 501
02AC2SOFTWARETRP A:228 , VAL A:245 , CYS A:249 , THR A:252 , THR A:253 , HIS A:287 , ILE A:290 , LEU A:294 , VAL A:305 , VAL A:312 , PHE A:316 , LEU A:317 , ILE A:328 , LYS A:331 , HIS A:413 , MET A:417 , LEU A:433 , TYR A:437 , HOH A:644binding site for residue 7SY A 502
03AC3SOFTWAREARG A:407binding site for residue PEG A 503
04AC4SOFTWARETHR A:256 , ILE A:290 , ILE A:297 , HOH A:648binding site for residue PGO A 504
05AC5SOFTWAREVAL A:257 , THR A:261 , LYS A:283 , GLU A:435 , ILE A:436 , LYS A:438 , B7G A:501 , LEU B:275 , ASN B:276 , HOH B:604 , HOH B:686binding site for residue B7G B 501
06AC6SOFTWARELEU B:219 , TRP B:228 , VAL B:245 , CYS B:249 , THR B:252 , THR B:253 , HIS B:287 , ILE B:290 , LEU B:294 , VAL B:305 , VAL B:312 , PHE B:316 , ILE B:328 , HIS B:413 , MET B:417 , LEU B:433 , TYR B:437 , HOH B:638binding site for residue 7SY B 502
07AC7SOFTWAREARG B:407binding site for residue PEG B 503
08AC8SOFTWAREPRO B:236 , CYS B:251 , GLU B:255 , ARG B:258 , SER B:428 , LEU B:429 , HIS B:430binding site for residue B7G B 504
09AC9SOFTWAREILE B:290binding site for residue PGO B 505
10AD1SOFTWARETYR B:183 , LEU B:187 , THR B:193 , GLU B:412 , GLN B:415 , MET B:416binding site for residue PEG B 506
11AD2SOFTWARETYR B:238 , ILE B:241 , HIS B:244binding site for residue PEG B 507

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5U45)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Lys A:322 -Pro A:323
2Lys B:322 -Pro B:323

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5U45)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5U45)

(-) Exons   (0, 0)

(no "Exon" information available for 5U45)

(-) 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 hhhhhhhhhhhhhhhhh..hhhhhhhhh...eee.hhhhhhhhhhhh....hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee..eeee....eeeehhhhhh........hhhhhhhhhhhhh...hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5u45 A 174 DLKAFSKHIYNAYLKNFNMTKKKARSILTAPFVIHDIETLWQAEKGLVWKQLVNGLPPYKEISVHVFYRCQCTTVETVRELTEFAKSIPSFSSLFLNDQVTLLKYGVHEAIFAMLASIVNKDGLLVANGSGFVTREFLRSLRKPFSDIIEPKFEFAVKFNALELDDSDLALFIAAIILCGDRPGLMNVPRVEAIQDTILRALEFHLQANHPDAQYLFPKLLQKMADLRQLVTEHAQMMQRIKKTETETSLHPLLQEIYKDMY 441
                                   183       193       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439  
                                                      202|                                                                                                                                                                                                                                        
                                                       209                                                                                                                                                                                                                                        

Chain B from PDB  Type:PROTEIN  Length:265
                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh..hhhhhhhhhhh.....eee.hhhhhhhhhhhh....hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..ee..eeeehhh.eeeehhhhhh...hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5u45 B 173 ADLKAFSKHIYNAYLKNFNMTKKKARSILTGKHTAPFVIHDIETLWQAEKGLVWKQLVNGLPPYKEISVHVFYRCQCTTVETVRELTEFAKSIPSFSSLFLNDQVTLLKYGVHEAIFAMLASIVNKDGLLVANGSGFVTREFLRSLRKPFSDIIEPKFEFAVKFNALELDDSDLALFIAAIILCGDRPGLMNVPRVEAIQDTILRALEFHLQANHPDAQYLFPKLLQKMADLRQLVTEHAQMMQRIKKTETETSLHPLLQEIYKD 439
                                   182       192       202 ||    214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434     
                                                         204|                                                                                                                                                                                                                                        
                                                          207                                                                                                                                                                                                                                        

   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 5U45)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5U45)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5U45)

(-) Gene Ontology  (81, 81)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        PPARD_HUMAN | Q031811gwx 1y0s 2awh 2b50 2baw 2env 2gwx 2j14 2q5g 2xyj 2xyw 2xyx 2znp 2znq 3d5f 3dy6 3et2 3gwx 3gz9 3oz0 3peq 3sp9 3tkm 5u3q 5u3r 5u3s 5u3t 5u3u 5u3v 5u3w 5u3x 5u3y 5u3z 5u40 5u41 5u42 5u43 5u44 5u46

(-) Related Entries Specified in the PDB File

5u3q 5u3r 5u3s 5u3t 5u3u 5u3v 5u3w 5u3x 5u3y 5u3z 5u40 5u41 5u42 5u43 5u44 5u46