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(-) Description

Title :  CRYSTAL STRUCTURE OF RARBETA LBD IN COMPLEX WITH AGONIST BMS411 [4-{[(5,5-DIMETHYL-8-PHENYL-5,6-DIHYDRONAPHTHALEN-2-YL) CARBONYL]AMINO}BENZOIC ACID]
 
Authors :  E. K. Nadendla, C. Teyssier, P. Germain, V. Delfosse, W. Bourguet
Date :  29 Mar 13  (Deposition) - 19 Mar 14  (Release) - 13 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym./Biol. Unit :  A,B,F,G
Keywords :  Ligand Binding Domain, Nuclear Hormone Receptor, Transcription- Agonist Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Nadendla, C. Teyssier, V. Delfosse, V. Vivat, G. Krishnasamy, H. Gronemeyer, W. Bourguet, P. Germain
An Unexpected Mode Of Binding Defines Bms948 As A Full Retinoic Acid Receptor Beta (Rar Beta , Nr1B2) Selective Agonist.
Plos One V. 10 23195 2015
PubMed-ID: 25933005  |  Reference-DOI: 10.1371/JOURNAL.PONE.0123195

(-) Compounds

Molecule 1 - RETINOIC ACID RECEPTOR BETA
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21-DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: LIGAND BINDING DOMAIN, UNP RESIDUES 176-421
    Gene: RARB, HAP, NR1B2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: RAR-BETA, HBV-ACTIVATED PROTEIN, NUCLEAR RECEPTOR SUBFAMILY 1 GROUP B MEMBER 2, RAR-EPSILON
 
Molecule 2 - STEROID RECEPTOR COACTIVATOR 1
    Chains: F, G
    EC Number: 2.3.1.48
    Engineered: YES
    Fragment: UNP RESIDUES 686-698
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SRC-1
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABFG

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
11NY2Ligand/Ion4-{[(5,5-DIMETHYL-8-PHENYL-5,6-DIHYDRONAPHTHALEN-2-YL)CARBONYL]AMINO}BENZOIC ACID
2FLC1Ligand/IonCITRATE ANION
3PE41Ligand/Ion2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:221 , ALA A:225 , LEU A:262 , ILE A:266 , ARG A:269 , PHE A:279 , SER A:280 , PHE A:295 , VAL A:302 , GLY A:384 , HOH A:716BINDING SITE FOR RESIDUE 1NY A 501
2AC2SOFTWAREGLU A:273 , ARG B:212 , LEU B:213 , LEU B:215 , HOH B:645 , HOH B:648BINDING SITE FOR RESIDUE PE4 B 501
3AC3SOFTWAREPHE B:192 , TRP B:218 , PHE B:221 , ALA B:225 , CYS B:228 , LEU B:262 , ILE B:266 , ARG B:269 , PHE B:279 , SER B:280 , VAL B:302 , LEU B:391 , HOH B:629BINDING SITE FOR RESIDUE 1NY B 502
4AC4SOFTWAREGLU A:337 , PRO A:338 , THR A:339 , HIS G:630 , LYS G:631 , ILE G:632 , ARG G:635 , HOH G:804 , HOH G:807 , HOH G:808BINDING SITE FOR RESIDUE FLC G 701

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4JYG)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4JYG)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4JYG)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4JYG)

(-) Exons   (0, 0)

(no "Exon" information available for 4JYG)

(-) 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:239
                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh...hhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee....eee.....eeehhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jyg A 170 SYEMTAELDDLTEKIRKAHQETFPSLCQLGKYTTNSSADHRVRLDLGLWDKFSELATKCIIKIVEFAKRLPGFTGLTIADQITLLKAACLDILILRICTRYTPEQDTMTFSDGLTLNRTQMHNAGFGPLTDLVFTFANQLLPLEMDDTETGLLSAICLICGDRQDLEEPTKVDKLQEPLLEALKIYIRKRRPSKPHMFPKILMKITDLRSISAKGAERVITLKMEIPGSMPPLIQEMME 408
                                   179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399         


Chain B from PDB  Type:PROTEIN  Length:240
                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhh.......................hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee....eee.....eeehhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4jyg B 169 ESYEMTAELDDLTEKIRKAHQETFPSLCQLGKYTTNSSADHRVRLDLGLWDKFSELATKCIIKIVEFAKRLPGFTGLTIADQITLLKAACLDILILRICTRYTPEQDTMTFSDGLTLNRTQMHNAGFGPLTDLVFTFANQLLPLEMDDTETGLLSAICLICGDRQDLEEPTKVDKLQEPLLEALKIYIRKRRPSKPHMFPKILMKITDLRSISAKGAERVITLKMEIPGSMPPLIQEMME 408
                                   178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408


Chain F 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
                 4jyg F 629 RHKILHRLLQE 639
                                   638 


Chain G from PDB  Type:PROTEIN  Length:11
                                           
               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
                 4jyg G 629 RHKILHRLLQE 639
                                   638
   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 4JYG)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4JYG)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4JYG)

(-) Gene Ontology  (92, 104)

Asymmetric/Biological Unit(hide GO term definitions)

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  NCOA1_HUMAN | Q15788
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  RARB_HUMAN | P10826
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 Related Entries

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

UniProtKB/Swiss-Prot
        NCOA1_HUMAN | Q15788: 1fm6 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 4jyh 4jyi 4mg5 4mg6 4mg7 4mg8 4mg9 4mga 4mgb 4mgc 4mgd 4ruj 4rup 4tuz 4tv1 4uda 4udb 4y29 5a86 5avi 5avl 5azt 5dsh 5dv3 5dv6 5dv8 5dvc 5dwl 5e7v 5hjs 5ji0 5jmm 5l7e 5l7g 5l7h 5nma 5x8u 5x8w
        RARB_HUMAN | P10826: 1hra 1xap 4dm6 4dm8 4jyh 4jyi

(-) Related Entries Specified in the PDB File

1xap 4dm6 4dm8 4jyh 4jyi