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(-) Description

Title :  CRYSTAL STRUCTURE OF THE RETINOIC ACID RECEPTOR ALPHA IN COMPLEX WITH A SYNTHETIC SPIROKETAL AGONIST AND A FRAGMENT OF THE TIF2 CO-ACTIVATOR.
 
Authors :  S. A. Andrei, C. Ottmann
Date :  28 Sep 16  (Deposition) - 26 Apr 17  (Release) - 10 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.17
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Nuclear Receptor, Rxr, Spiroketal, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Scheepstra, S. A. Andrei, M. Y. Unver, A. K. H. Hirsch, S. Leysen, C. Ottmann, L. Brunsveld, L. G. Milroy
Designed Spiroketal Protein Modulation.
Angew. Chem. Int. Ed. Engl. V. 56 5480 2017
PubMed-ID: 28407400  |  Reference-DOI: 10.1002/ANIE.201612504

(-) Compounds

Molecule 1 - RETINOIC ACID RECEPTOR RXR-ALPHA
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET15B
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 223-462
    Gene: RXRA, NR2B1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: NUCLEAR RECEPTOR SUBFAMILY 2 GROUP B MEMBER 1,RETINOID X RECEPTOR ALPHA
 
Molecule 2 - HIS-LYS-ILE-LEU-HIS-ARG-LEU-LEU-GLN-ASP
    Chains: B
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
17BE1Ligand/Ion(2~{R})-6,6,9,9-TETRAMETHYLSPIRO[3,4,7,8-TETRAHYDROBENZO[G]CHROMENE-2,2'-3,4-DIHYDROCHROMENE]-6'-CARBOXYLIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:268 , ALA A:271 , ALA A:272 , ASN A:306 , LEU A:309 , ILE A:310 , PHE A:313 , ARG A:316 , LEU A:326 , ALA A:327 , CYS A:432 , HIS A:435binding site for residue 7BE A 501

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5LYQ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5LYQ)

(-) Sequences/Alignments

Asymmetric/Biological 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:212
                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh.....eee.....eeehhhhhh..hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lyq A 229 DMPVERILEAELAVEPDPVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLMEMLEAP 458
                                   238     ||266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456  
                                         244|                                                                                                                                                                                                   
                                          263                                                                                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:10
                                          
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                 5lyq B 472 HKILHRLLQD 481
                                   481
   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 5LYQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (78, 78)

Asymmetric/Biological Unit(hide GO term definitions)

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  RXRA_HUMAN | P19793
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 Related Entries

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

UniProtKB/Swiss-Prot
        RXRA_HUMAN | P19793: 1by4 1dsz 1fby 1fm6 1fm9 1g1u 1g5y 1k74 1lbd 1mv9 1mvc 1mzn 1r0n 1rdt 1rxr 1xls 1xv9 1xvp 1ynw 2acl 2nll 2p1t 2p1u 2p1v 2zxz 2zy0 3dzu 3dzy 3e00 3e94 3fal 3fc6 3fug 3h0a 3kwy 3nsp 3nsq 3oap 3ozj 3pcu 3r29 3r2a 3r5m 3uvv 4cn2 4cn3 4cn5 4cn7 4j5w 4j5x 4k4j 4k6i 4m8e 4m8h 4n5g 4n8r 4nqa 4oc7 4poh 4poj 4pp3 4pp5 4rfw 4rmc 4rmd 4rme 4zo1 4zsh 5ec9 5ji0

(-) Related Entries Specified in the PDB File

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