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(-) Description

Title :  HUMAN PPARDELTA LIGAND-BINDING DOMAIN IN COMPLEXED WITH SPECIFIC AGONIST 5
 
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 :  2.10
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
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28A(+)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PPARD, NR1C2, PPARB
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: LIGAND-BINDING DOMAIN
    Synonym: PPAR-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, 5)

Asymmetric Unit (4, 5)
No.NameCountTypeFull Name
17TV1Ligand/Ion6-[2-({CYCLOPENTYL[4-(FURAN-2-YL)BENZENE-1-CARBONYL]AMINO}METHYL)PHENOXY]HEXANOIC ACID
2B7G2Ligand/IonHEPTYL-BETA-D-GLUCOPYRANOSIDE
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
4PGO1Ligand/IonS-1,2-PROPANEDIOL
Biological Unit 1 (4, 4)
No.NameCountTypeFull Name
17TV1Ligand/Ion6-[2-({CYCLOPENTYL[4-(FURAN-2-YL)BENZENE-1-CARBONYL]AMINO}METHYL)PHENOXY]HEXANOIC ACID
2B7G1Ligand/IonHEPTYL-BETA-D-GLUCOPYRANOSIDE
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
4PGO1Ligand/IonS-1,2-PROPANEDIOL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
17TV-1Ligand/Ion6-[2-({CYCLOPENTYL[4-(FURAN-2-YL)BENZENE-1-CARBONYL]AMINO}METHYL)PHENOXY]HEXANOIC ACID
2B7G1Ligand/IonHEPTYL-BETA-D-GLUCOPYRANOSIDE
3PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
4PGO-1Ligand/IonS-1,2-PROPANEDIOL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:219 , TRP A:228 , VAL A:245 , ARG A:248 , CYS A:249 , THR A:252 , THR A:253 , HIS A:287 , ILE A:290 , LEU A:303 , ILE A:328 , LYS A:331 , HIS A:413 , MET A:417 , LEU A:433 , TYR A:437 , PGO A:502 , HOH A:617binding site for residue 7TV A 501
2AC2SOFTWARETHR A:256 , ILE A:290 , LEU A:294 , 7TV A:501binding site for residue PGO A 502
3AC3SOFTWAREGLU A:217 , TRP A:220 , GLN A:221binding site for residue PEG A 503
4AC4SOFTWARETHR A:261 , LYS A:283 , GLU A:435 , ILE A:436 , LYS A:438 , ASN B:276 , VAL B:279 , THR B:280 , B7G B:501binding site for residue B7G A 504
5AC5SOFTWAREASN A:276 , VAL A:279 , THR A:280 , B7G A:504 , HOH A:609 , LYS B:283 , LEU B:432 , GLU B:435 , ILE B:436binding site for residue B7G B 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5U3U)

(-) 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 5U3U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5U3U)

(-) Exons   (0, 0)

(no "Exon" information available for 5U3U)

(-) 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:255
                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh..hhhhhhhhh...eee.hhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..ee..eeee....eeeehhhhhhh.......hhhhhhhhhhhhh...hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5u3u A 172 VADLKAFSKHIYNAYLKNFNMTKKKARSILTAPFVIHDIETLWQAEKVWGLPPYKEISVHVFYRCQCTTVETVRELTEFAKSIPSFSSLFLNDQVTLLKYGVHEAIFAMLASIVNKDGLLVANGSGFVTREFLRSLRKPFSDIIEPKFEFAVKFNALELDDSDLALFIAAIILCGDRPGLMNVPRVEAIQDTILRALEFHLQANHPDAQYLFPKLLQKMADLRQLVTEHAQMMQRIKKTETETSLHPLLQEIYKD 439
                                   181       191       201||     217      |234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434     
                                                        202|            224|||                                                                                                                                                                                                             
                                                         209             227||                                                                                                                                                                                                             
                                                                          228|                                                                                                                                                                                                             
                                                                           234                                                                                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:250
                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh..hhhhhhh.....eee.hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee..eeee....eeeehhhhhhh.......hhhhhhhhhhhhhhh.hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5u3u B 174 DLKAFSKHIYNAYLKNFNMTKKKARSILTAPFVIHDIETLWQAEKGLLPPYKEISVHVFYRCQCTTVETVRELTEFAKSIPSFSSLFLNDQVTLLKYGVHEAIFAMLASIVNKDGLLVANGSGFVTREFLRSLRKPFSDIIEPKFEFAVKFNALELDDSDLALFIAAIILCGDRPGLMNVPRVEAIQDTILRALEFHLQANHPDAQYLFPKLLQKMADLRQLVTEHAQMMQRIKKTETETSLHPLLQEIY 437
                                   183       193       209       219      |237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437
                                                      202|              226|                                                                                                                                                                                                          
                                                       209               235
   Legend:   → Mismatch (orange background)
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  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 5U3U)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5U3U)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5U3U)

(-) Gene Ontology  (81, 81)

Asymmetric Unit(hide GO term definitions)

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  PPARD_HUMAN | Q03181
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 Related Entries

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

UniProtKB/Swiss-Prot
        PPARD_HUMAN | Q03181: 1gwx 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 5u3v 5u3w 5u3x 5u3y 5u3z 5u40 5u41 5u42 5u43 5u44 5u45 5u46

(-) Related Entries Specified in the PDB File

5u3q 5u3r 5u3s 5u3t 5u3v 5u3w 5u3x 5u3y 5u3z 5u40 5u41 5u42 5u44 5u45 5u46