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(-) Description

Title :  STRUCTURAL BASIS FOR THE ACCOMMODATION OF BIS- AND TRIS-AROMATIC DERIVATIVES IN VITAMIN D NUCLEAR RECEPTOR
 
Authors :  F. Ciesielski, Y. Sato, D. Moras, N. . Rochel
Date :  10 Jul 12  (Deposition) - 26 Sep 12  (Release) - 21 Nov 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  Transcription Regulation, Vdr, Vitamin D, Alpha Helical Sandwich, Transcription, Ligand, Adn, Phosphorylation, Nucleus, Transcription- Transcription Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Ciesielski, Y. Sato, Y. Chebaro, D. Moras, A. Dejaegere, N. Rochel
Structural Basis For The Accommodation Of Bis- And Tris-Aromatic Derivatives In Vitamin D Nuclear Receptor.
J. Med. Chem. V. 55 8440 2012
PubMed-ID: 22957834  |  Reference-DOI: 10.1021/JM300858S

(-) Compounds

Molecule 1 - VITAMIN D3 RECEPTOR A
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21DE3
    Expression System Taxid: 562
    Expression System Vector Type: PET28
    Fragment: UNP RESIDUES 156-453
    Gene: VDRA, NR1I1A, VDR
    Organism Common: LEOPARD DANIO,ZEBRA DANIO,ZEBRA FISH
    Organism Scientific: DANIO RERIO
    Organism Taxid: 7955
    Synonym: VDR-A, 1,25-DIHYDROXYVITAMIN D3 RECEPTOR A, NUCLEAR RECEPTOR SUBFAMILY 1 GROUP I MEMBER 1-A
 
Molecule 2 - NUCLEAR RECEPTOR COACTIVATOR 1
    Chains: B
    Engineered: YES
    Fragment: UNP RESIDUES 686-700
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: NCOA-1,CLASS E BASIC HELIX-LOOP-HELIX PROTEIN 74, BHLHE74, STEROID RECEPTOR COACTIVATOR 1, RENAL CARCINOMA ANTIGEN NY-REN-52
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (2x): AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
10VK1Ligand/Ion3-(5'-{[3,4-BIS(HYDROXYMETHYL)BENZYL]OXY}-2'-METHYL-2-PROPYLBIPHENYL-4-YL)PENTAN-3-OL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
10VK1Ligand/Ion3-(5'-{[3,4-BIS(HYDROXYMETHYL)BENZYL]OXY}-2'-METHYL-2-PROPYLBIPHENYL-4-YL)PENTAN-3-OL
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
10VK2Ligand/Ion3-(5'-{[3,4-BIS(HYDROXYMETHYL)BENZYL]OXY}-2'-METHYL-2-PROPYLBIPHENYL-4-YL)PENTAN-3-OL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:175 , ALA A:259 , LEU A:261 , SER A:265 , ILE A:296 , MET A:300 , ARG A:302 , SER A:303 , SER A:306 , TRP A:314 , VAL A:328 , HIS A:333 , LEU A:338 , HIS A:423 , TYR A:427 , LEU A:440BINDING SITE FOR RESIDUE 0VK A 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4G1D)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4G1D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4G1D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4G1D)

(-) Exons   (0, 0)

(no "Exon" information available for 4G1D)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
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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 ...hhhhhhhhhhhhhhhhhhh...hhhhhhh........hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh..ee....eee......ee..hhhhhhh.hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g1d A 154 HMLSDEQMQIINSLVEAHHKTYDDSYSDFVRFRPPVRRLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTAEDQIALLKSSAIEIIMLRSNQSFSLEDMSWSCGGPDFKYCINDVTKAGHTLELLEPLVKFQVGLKKLKLHEEEHVLLMAICLLSPDRPGVQDHVRIEALQDRLCDVLQAYIRIQHPGGRLLYAKMIQKLADLRSLNEEHSKQYRSLSFQPEHSMQLTPLVLEVFGSEV 452
                                   163       173       183      |253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443         
                                                              190|                                                                                                                                                                                                         
                                                               251                                                                                                                                                                                                         


Chain B 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
                 4g1d B 686 RHKILHRLLQE 696
                                   695
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  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 4G1D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4G1D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4G1D)

(-) Gene Ontology  (75, 81)

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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 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 5azt 5dsh 5dv3 5dv6 5dv8 5dvc 5dwl 5e7v 5hjs 5ji0 5jmm 5l7e 5l7g 5l7h 5nma 5x8u 5x8w
        VDRA_DANRE | Q9PTN2: 2hbh 2hc4 2hcd 3dr1 3o1d 3o1e 4fhh 4fhi 4g1y 4g1z 4g20 4g21 4g2h 4ia1 4ia2 4ia3 4ia7 4q0a 4ruj 4ruo 4rup 5e7v 5lga 5nky 5nma

(-) Related Entries Specified in the PDB File

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