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(-) Description

Title :  HUMAN PPARDELTA LIGAND-BINDING DOMAIN IN COMPLEXED WITH SPECIFIC AGONIST 9
 
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 :  1.90
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, 13)

Asymmetric Unit (4, 13)
No.NameCountTypeFull Name
17U72Ligand/Ion6-[2-({CYCLOPROPYL[4-(FURAN-2-YL)BENZENE-1-CARBONYL]AMINO}METHYL)PHENOXY]HEXANOIC ACID
2B7G2Ligand/IonHEPTYL-BETA-D-GLUCOPYRANOSIDE
3PEG6Ligand/IonDI(HYDROXYETHYL)ETHER
4PGO3Ligand/IonS-1,2-PROPANEDIOL
Biological Unit 1 (4, 7)
No.NameCountTypeFull Name
17U71Ligand/Ion6-[2-({CYCLOPROPYL[4-(FURAN-2-YL)BENZENE-1-CARBONYL]AMINO}METHYL)PHENOXY]HEXANOIC ACID
2B7G2Ligand/IonHEPTYL-BETA-D-GLUCOPYRANOSIDE
3PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
4PGO2Ligand/IonS-1,2-PROPANEDIOL
Biological Unit 2 (3, 6)
No.NameCountTypeFull Name
17U71Ligand/Ion6-[2-({CYCLOPROPYL[4-(FURAN-2-YL)BENZENE-1-CARBONYL]AMINO}METHYL)PHENOXY]HEXANOIC ACID
2B7G-1Ligand/IonHEPTYL-BETA-D-GLUCOPYRANOSIDE
3PEG4Ligand/IonDI(HYDROXYETHYL)ETHER
4PGO1Ligand/IonS-1,2-PROPANEDIOL

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:275 , ASN A:276 , VAL A:279 , THR A:280 , B7G A:507 , HOH A:607 , THR B:261 , LYS B:283 , GLU B:435 , ILE B:436 , LYS B:438binding site for residue B7G A 501
02AC2SOFTWAREVAL A:245 , ARG A:248 , CYS A:249 , THR A:252 , THR A:253 , HIS A:287 , ILE A:290 , LEU A:294 , VAL A:305 , VAL A:312 , LYS A:331 , HIS A:413 , LEU A:433 , TYR A:437 , HOH A:606binding site for residue 7U7 A 502
03AC3SOFTWARELYS A:283 , TYR A:284 , VAL A:410 , ILE A:436 , TYR A:437 , HOH A:625binding site for residue PGO A 503
04AC4SOFTWARETHR A:252 , HOH A:610binding site for residue PGO A 504
05AC5SOFTWARELEU A:400 , ARG A:407binding site for residue PEG A 505
06AC6SOFTWARESER A:428 , LEU A:429 , GLN A:434binding site for residue PEG A 506
07AC7SOFTWARETHR A:261 , LYS A:283 , GLU A:435 , ILE A:436 , LYS A:438 , B7G A:501 , LEU B:275 , ASN B:276 , VAL B:279 , THR B:280 , HOH B:632binding site for residue B7G A 507
08AC8SOFTWARETRP B:228 , VAL B:245 , ARG B:248 , CYS B:249 , THR B:252 , THR B:253 , HIS B:287 , LEU B:294 , VAL B:305 , ILE B:328 , LYS B:331 , HIS B:413 , MET B:417 , LEU B:433 , TYR B:437 , HOH B:621binding site for residue 7U7 B 501
09AC9SOFTWAREARG B:407binding site for residue PGO B 502
10AD1SOFTWAREMET B:192 , MET B:293 , HOH B:608binding site for residue PEG B 503
11AD2SOFTWARETYR B:394binding site for residue PEG B 504
12AD3SOFTWARETYR B:238binding site for residue PEG B 505
13AD4SOFTWARETHR A:261 , GLU A:262 , SER B:272 , LEU B:273 , PHE B:274 , LEU B:275binding site for residue PEG B 506

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5U3Y)

(-) 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 5U3Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5U3Y)

(-) Exons   (0, 0)

(no "Exon" information available for 5U3Y)

(-) 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:263
                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh..hhhhhhhhhh........eee.hhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..ee..eeee....eeeehhhhhh........hhhhhhhhhhhhh...hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5u3y A 171 QVADLKAFSKHIYNAYLKNFNMTKKKARSILTGKASHTAPFVIHDIETLWQAEKGLVWLPPYKEISVHVFYRCQCTTVETVRELTEFAKSIPSFSSLFLNDQVTLLKYGVHEAIFAMLASIVNKDGLLVANGSGFVTREFLRSLRKPFSDIIEPKFEFAVKFNALELDDSDLALFIAAIILCGDRPGLMNVPRVEAIQDTILRALEFHLQANHPDAQYLFPKLLQKMADLRQLVTEHAQMMQRIKKTETETSLHPLLQEIYKD 439
                                   180       190       200       210       220       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436   
                                                                                   228|                                                                                                                                                                                                            
                                                                                    235                                                                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:255
                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh..hhhhhhhhh...eee.hhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh...ee..eeeehhh.eeeehhhhhh........hhhhhhhhhhhhh...hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5u3y B 173 ADLKAFSKHIYNAYLKNFNMTKKKARSILTAPFVIHDIETLWQAEKGLVWLPPYKEISVHVFYRCQCTTVETVRELTEFAKSIPSFSSLFLNDQVTLLKYGVHEAIFAMLASIVNKDGLLVANGSGFVTREFLRSLRKPFSDIIEPKFEFAVKFNALELDDSDLALFIAAIILCGDRPGLMNVPRVEAIQDTILRALEFHLQANHPDAQYLFPKLLQKMADLRQLVTEHAQMMQRIKKTETETSLHPLLQEIYKD 439
                                   182       192       202|      218       228|      244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434     
                                                       202|                228|                                                                                                                                                                                                            
                                                        209                 235
   Legend:   → Mismatch (orange background)
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    → 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 5U3Y)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5U3Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5U3Y)

(-) 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 5u3u 5u3v 5u3w 5u3x 5u3z 5u40 5u41 5u42 5u43 5u44 5u45 5u46

(-) Related Entries Specified in the PDB File

5u3q 5u3r 5u3s 5u3t 5u3u 5u3v 5u3w 5u3x 5u3y 5u3z 5u40 5u41 5u42 5u44 5u45 5u46