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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN RETINOID X RECEPTOR ALPHA-LIGAND BINDING DOMAIN COMPLEX WITH 5-METHYL UAB30 AND THE COACTIVATOR PEPTIDE GRIP-1
 
Authors :  G. Xia, C. D. Smith, D. D. Muccio
Date :  26 Feb 14  (Deposition) - 18 Jun 14  (Release) - 23 Jul 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ligand Binding Domain. 6-Methyl Uab30, Rexinoid, Cancer, Lipid Toxicity, Ligand Binding Domain, 6-Methyl Uab30, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. R. Atigadda, G. Xia, A. Desphande, L. J. Boerma, S. Lobo-Ruppert, C. J. Grubbs, C. D. Smith, W. J. Brouillette, D. D. Muccio
Methyl Substitution Of A Rexinoid Agonist Improves Potency And Reveals Site Of Lipid Toxicity.
J. Med. Chem. V. 57 5370 2014
PubMed-ID: 24801499  |  Reference-DOI: 10.1021/JM5004792

(-) Compounds

Molecule 1 - RETINOIC ACID RECEPTOR RXR-ALPHA
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 469008
    Expression System Vector Type: BL21(DE3)
    Fragment: LIGAND BINDING DOMAIN, UNP RESIDUES 228-458
    Gene: NR2B1, RXRA, RXRA NR2B1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Strain: P19793
    Synonym: NUCLEAR RECEPTOR SUBFAMILY 2 GROUP B MEMBER 1, RETINOID X RECEPTOR ALPHA
 
Molecule 2 - NUCLEAR RECEPTOR COACTIVATOR 2
    Chains: B
    Engineered: YES
    Fragment: COACTIVATOR PEPTIDE, UNP RESIDUES 686-698
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: NCOA-2, CLASS E BASIC HELIX-LOOP-HELIX PROTEIN 75, BHLHE75, TRANSCRIPTIONAL INTERMEDIARY FACTOR 2, HTIF2
    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
12W01Ligand/Ion(2E,4E,6Z,8E)-3,7-DIMETHYL-8-(5-METHYL-3,4-DIHYDRONAPHTHALEN-1(2H)-YLIDENE)OCTA-2,4,6-TRIENOICACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:271 , ALA A:272 , GLN A:275 , PHE A:313 , ARG A:316 , LEU A:326 , ALA A:327 , VAL A:342 , ILE A:345 , LEU A:436 , HOH A:612BINDING SITE FOR RESIDUE 2W0 A 500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4PP5)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ala A:457 -Pro A:458

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4PP5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4PP5)

(-) Exons   (0, 0)

(no "Exon" information available for 4PP5)

(-) 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:214
                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee.....eeehhhhhhh.hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pp5 A 228 EDMPVERILEAELAVEPNDPVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLMEMLEAP 458
                                   237      |264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454    
                                          244|                                                                                                                                                                                                    
                                           262                                                                                                                                                                                                    


Chain B 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
                 4pp5 B 686 KHKILHRLLQD 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 4PP5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4PP5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4PP5)

(-) Gene Ontology  (119, 132)

Asymmetric/Biological Unit(hide GO term definitions)

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  NCOA2_HUMAN | Q15596
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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
        NCOA2_HUMAN | Q15596: 1gwq 1gwr 1m2z 1mv9 1mvc 1mzn 1p93 1t63 1t65 1uhl 1yok 1zdt 1zdu 1zky 2ao6 2b1v 2b1z 2b23 2fai 2g44 2g5o 2ldc 2p15 2p1t 2p1u 2p1v 2q7j 2q7l 2yjd 2zxz 2zy0 3a9e 3cld 3dzu 3dzy 3e00 3e7c 3e94 3erd 3fug 3gn8 3k22 3k23 3kwy 3kyt 3l0e 3l0j 3l0l 3o1d 3o1e 3oap 3ozj 3pcu 3plz 3q95 3q97 3r5m 3up0 3up3 4csj 4dos 4e2j 4fhh 4fhi 4ia1 4ia2 4ia3 4ia7 4iqr 4iu7 4iui 4iv2 4iv4 4ivw 4ivy 4iw6 4iw8 4iwc 4iwf 4k4j 4k6i 4m8e 4m8h 4nie 4nqa 4oc7 4p6w 4p6x 4pld 4ple 4poh 4poj 4pp3 4pp6 4ppp 4pps 4pxm 4q0a 4qe6 4qe8 4rfw 4rmc 4rmd 4rme 4ruo 4udc 4udd 4wg0 4zn7 4zn9 4znh 4zns 4znt 4znu 4znv 4znw 4zo1 4zsh 5aph 5apj 5di7 5did 5die 5dig 5dk9 5dkb 5dke 5dkg 5dks 5dl4 5dlr 5dmc 5dmf 5dp0 5drj 5drm 5dtv 5du5 5due 5dug 5duh 5dvs 5dvv 5dwe 5dwg 5dwi 5dwj 5dx3 5dxb 5dxe 5dxg 5dxk 5dxm 5dxp 5dxq 5dxr 5dy8 5dyb 5dyd 5dz0 5dz1 5dz3 5dzh 5dzi 5e0w 5e0x 5e14 5e15 5e19 5e1c 5ec9 5egv 5ehj 5ei1 5eit 5g3j 5g42 5g43 5g44 5g45 5g46 5g5w 5h1e 5hyr 5i4v 5iaw 5ick 5kcc 5kcd 5kce 5kcf 5kct 5kcu 5kcw 5kd9 5kr9 5kra 5krc 5krf 5krh 5kri 5krj 5krk 5krl 5krm 5kro 5l11 5lga 5syz 5tld 5tlf 5tlg 5tll 5tlm 5tlo 5tlp 5tlt 5tlu 5tlv 5tlx 5tly 5tm1 5tm2 5tm3 5tm4 5tm5 5tm6 5tm7 5tm8 5tm9 5tml 5tmm 5tmo 5tmq 5tmr 5tms 5tmt 5tmu 5tmv 5tmw 5tmz 5tn1 5tn3 5tn4 5tn5 5tn6 5tn7 5tn8 5u2d
        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 4rfw 4rmc 4rmd 4rme 4zo1 4zsh 5ec9 5ji0 5lyq

(-) Related Entries Specified in the PDB File

3oap 4k4j 4poh 4poj 4pp3