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(-) Description

Title :  TERNARY COMPLEX OF HPPARALPHA LIGAND BINDING DOMAIN, 17-OXODHA AND A SRC1 PEPTIDE
 
Authors :  D. Egawa, T. Itoh, K. Yamamoto
Date :  23 Oct 15  (Deposition) - 06 Jul 16  (Release) - 13 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.45
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Nuclear Receptor, Transcription Regulation, Ligand Binding Domain, Zinc-Finger, Dna Binding, Transcription, Obesity, Nucleus, Receptor, Activator, Oxidized Fatty Acid, Transcription Factor, Agonist, Dual Agonist, Covalent, Ppre, Nuclear, Co-Activator, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. Egawa, T. Itoh, Y. Akiyama, T. Saito, K. Yamamoto
17-Oxodha Is A Ppar Alpha/Gamma Dual Covalent Modifier And Agonist
Acs Chem. Biol. 2016
PubMed-ID: 27337155  |  Reference-DOI: 10.1021/ACSCHEMBIO.6B00338

(-) Compounds

Molecule 1 - PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR ALPHA
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 201-468
    GenePPARA, NR1C1, PPAR
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPPAR-ALPHA,NUCLEAR RECEPTOR SUBFAMILY 1 GROUP C MEMBER 1
 
Molecule 2 - 15-MERIC PEPTIDE FROM NUCLEAR RECEPTOR COACTIVATOR 1
    ChainsC
    EngineeredYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SyntheticYES

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC
Biological Unit 1 (1x)A C
Biological Unit 2 (1x) B 

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
14M52Ligand/Ion(4~{Z},7~{Z},10~{Z},13~{Z},19~{Z})-17-OXIDANYLIDENEDOCOSA-4,7,10,13,19-PENTAENOIC ACID
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
14M51Ligand/Ion(4~{Z},7~{Z},10~{Z},13~{Z},19~{Z})-17-OXIDANYLIDENEDOCOSA-4,7,10,13,19-PENTAENOIC ACID
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
14M51Ligand/Ion(4~{Z},7~{Z},10~{Z},13~{Z},19~{Z})-17-OXIDANYLIDENEDOCOSA-4,7,10,13,19-PENTAENOIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:251 , CYS A:275 , CYS A:276 , THR A:279 , SER A:280 , TYR A:314 , ALA A:333 , GLY A:337 , HIS A:440 , TYR A:464binding site for residue 4M5 A 501
2AC2SOFTWARELEU B:247 , GLU B:251 , CYS B:275 , CYS B:276 , THR B:279 , SER B:280 , TYR B:314 , VAL B:332 , HIS B:440 , TYR B:464binding site for residue 4M5 B 501

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Lys A:349 -Pro A:350
2Leu A:368 -Glu A:369
3Lys B:349 -Pro B:350

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5AZT)

(-) 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:261
                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh..hhhhhhhhh.....eee.hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh......eeee....eeeehhhhhhh..hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5azt A 204 KSLAKRIYEAYLKNFNMNKVKARVILSNNPPFVIHDMETLCMAEKTLVAKLVANGIQNKEAEVRIFHCCQCTSVETVTELTEFAKAIPGFANLDLNDQVTLLKYGVYEAIFAMLSSVMNKDGMLVAYGNGFITREFLKSLRKPFCDIMEPKFDFAMKFNALELDDSDISLFVAAIICCGDRPGLLNVGHIEKMQEGIVHVLRLHLQSNHPDDIFLLPKLLQKMADLRQLVTEHAQLVQIIKKTESDAALHPLLQEIYRDMY 468
                                   213       223     ||237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467 
                                                   229|                                                                                                                                                                                                                                          
                                                    234                                                                                                                                                                                                                                          

Chain B from PDB  Type:PROTEIN  Length:251
                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh..hhhhhhhhhhh......eee.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh......eeee....eeeehhhhhhh..hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5azt B 204 KSLAKRIYEAYLKNFNMNKVKARVILSGKASNPPFVIHDMETLCMAEKTLKEAEVRIFHCCQCTSVETVTELTEFAKAIPGFANLDLNDQVTLLKYGVYEAIFAMLSSVMNKDGMLVAYGNGFITREFLKSLRKPFCDIMEPKFDFAMKFNALELDDSDISLFVAAIICCGDRPGLLNVGHIEKMQEGIVHVLRLHLQSNHPDDIFLLPKLLQKMADLRQLVTEHAQLVQIIKKTESDAALHPLLQEIYRD 466
                                   213       223       233||     244       254|      275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465 
                                                        234|               254|                                                                                                                                                                                                        
                                                         236                266                                                                                                                                                                                                        

Chain C from PDB  Type:PROTEIN  Length:11
                                           
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author .hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 5azt C 686 RHKILHRLLQE 696
                                   695 

   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 5AZT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (117, 128)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        NCOA1_HUMAN | Q157881fm6 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 4y29 5a86 5avi 5avl 5dsh 5dv3 5dv6 5dv8 5dvc 5dwl 5e7v 5hjs 5ji0 5jmm 5l7e 5l7g 5l7h 5nma 5x8u 5x8w
        PPARA_HUMAN | Q078691i7g 1k7l 1kkq 2npa 2p54 2rew 2znn 3et1 3fei 3g8i 3kdt 3kdu 3sp6 3vi8 4bcr 4ci4 5hyk

(-) Related Entries Specified in the PDB File

5azv