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(-) Description

Title :  IDENTIFICATION OF A NOVEL FXR LIGAND THAT REGULATES METABOLISM
 
Authors :  R. Wang, Y. Li
Date :  05 Nov 14  (Deposition) - 11 Feb 15  (Release) - 02 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Af-2 Helix, Ligand Binding Pocket, Three-Layer Helical Sandwich, Transcription Regulator Fxr, Bar, Nr1H4, Bile Acid Receptor, Nhr, Nuclear Receptor, Corepressor, Transcription, Transcription Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Jin, X. Feng, H. Rong, Z. Pan, Y. Inaba, L. Qiu, W. Zheng, S. Lin, R. Wang, Z. Wang, S. Wang, H. Liu, S. Li, W. Xie, Y. Li
The Antiparasitic Drug Ivermectin Is A Novel Fxr Ligand Tha Regulates Metabolism.
Nat Commun V. 4 1937 2013
PubMed-ID: 23728580  |  Reference-DOI: 10.1038/NCOMMS2924

(-) Compounds

Molecule 1 - NUCLEAR RECEPTOR COREPRESSOR 1
    ChainsC, D
    EngineeredYES
    FragmentUNP RESIDUES 2259-2275
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymN-COR1
    SyntheticYES
 
Molecule 2 - BILE ACID RECEPTOR
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET24
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentLIGAND BINDING DOMAIN, UNP RESIDUES 244-454
    GeneNR1H4, BAR, FXR, HRR1, RIP14
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymFARNESOID X-ACTIVATED RECEPTOR,FARNESOL RECEPTOR HRR-1, NUCLEAR RECEPTOR SUBFAMILY 1 GROUP H MEMBER 4,RETINOID X RECEPTOR- INTERACTING PROTEIN 14,RXR-INTERACTING PROTEIN 14

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A C 
Biological Unit 2 (1x) B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric Unit (2, 10)
No.NameCountTypeFull Name
1FMT8Ligand/IonFORMIC ACID
2IVM2Ligand/Ion(2AE,4E,5'S,6S,6'R,7S,8E,11R,13R,15S,17AR,20R,20AR,20BS)-6'-[(2S)-BUTAN-2-YL]-20,20B-DIHYDROXY-5',6,8,19-TETRAMETHYL-17-OXO-3',4',5',6,6',10,11,14,15,17,17A,20,20A,20B-TETRADECAHYDRO-2H,7H-SPIRO[11,15-METHANOFURO[4,3,2-PQ][2,6]BENZODIOXACYCLOOCTADECINE-13,2'-PYRAN]-7-YL 2,6-DIDEOXY-4-O-(2,6-DIDEOXY-3-O-METHYL-ALPHA-L-ARABINO-HEXOPYRANOSYL)-3-O-METHYL-ALPHA-L-ARABINO-HEXOPYRANOSIDE
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
1FMT4Ligand/IonFORMIC ACID
2IVM1Ligand/Ion(2AE,4E,5'S,6S,6'R,7S,8E,11R,13R,15S,17AR,20R,20AR,20BS)-6'-[(2S)-BUTAN-2-YL]-20,20B-DIHYDROXY-5',6,8,19-TETRAMETHYL-17-OXO-3',4',5',6,6',10,11,14,15,17,17A,20,20A,20B-TETRADECAHYDRO-2H,7H-SPIRO[11,15-METHANOFURO[4,3,2-PQ][2,6]BENZODIOXACYCLOOCTADECINE-13,2'-PYRAN]-7-YL 2,6-DIDEOXY-4-O-(2,6-DIDEOXY-3-O-METHYL-ALPHA-L-ARABINO-HEXOPYRANOSYL)-3-O-METHYL-ALPHA-L-ARABINO-HEXOPYRANOSIDE
Biological Unit 2 (2, 5)
No.NameCountTypeFull Name
1FMT4Ligand/IonFORMIC ACID
2IVM1Ligand/Ion(2AE,4E,5'S,6S,6'R,7S,8E,11R,13R,15S,17AR,20R,20AR,20BS)-6'-[(2S)-BUTAN-2-YL]-20,20B-DIHYDROXY-5',6,8,19-TETRAMETHYL-17-OXO-3',4',5',6,6',10,11,14,15,17,17A,20,20A,20B-TETRADECAHYDRO-2H,7H-SPIRO[11,15-METHANOFURO[4,3,2-PQ][2,6]BENZODIOXACYCLOOCTADECINE-13,2'-PYRAN]-7-YL 2,6-DIDEOXY-4-O-(2,6-DIDEOXY-3-O-METHYL-ALPHA-L-ARABINO-HEXOPYRANOSYL)-3-O-METHYL-ALPHA-L-ARABINO-HEXOPYRANOSIDE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREFMT A:502 , FMT A:504binding site for residue FMT A 501
02AC2SOFTWAREFMT A:501 , FMT A:503binding site for residue FMT A 502
03AC3SOFTWAREASP A:394 , FMT A:502binding site for residue FMT A 503
04AC4SOFTWARELEU A:434 , FMT A:501 , HOH A:601binding site for residue FMT A 504
05AC5SOFTWAREARG A:264 , LYS A:272 , GLU A:276 , ASN A:283 , LEU A:287 , MET A:290 , ALA A:291 , ASN A:293 , HIS A:294 , ARG A:331 , ILE A:335 , LEU A:348 , MET A:365binding site for residue IVM A 505
06AC6SOFTWARELEU B:434 , FMT B:502 , FMT B:504binding site for residue FMT B 501
07AC7SOFTWAREFMT B:501 , FMT B:504binding site for residue FMT B 502
08AC8SOFTWAREASP B:394binding site for residue FMT B 503
09AC9SOFTWAREFMT B:501 , FMT B:502binding site for residue FMT B 504
10AD1SOFTWAREARG B:264 , LYS B:272 , GLU B:276 , ASN B:283 , LEU B:287 , MET B:290 , ASN B:293 , SER B:332 , PHE B:336 , LEU B:347 , LEU B:348 , TYR B:361 , MET B:365binding site for residue IVM B 505

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Leu C:2261 -Gly C:2262
2Arg A:264 -Met A:265
3His A:344 -Ser A:345
4Ser A:355 -Gly A:356
5Ser A:453 -Trp A:454
6Arg B:264 -Met B:265

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4WVD)

(-) 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:210
                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh..hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhh........hhhhhhhhhhhhhh...hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4wvd A  244 ELTPDQQTLLHFIMDSYNKQRMPQEITNKILKEFSAEENFLILTEMATNHVQVLVEFTKKLPGFQTLDHEDQIALLKGSAVEAMFLRSAEIFNKKLPSGHSDLLEERIRNSGISDEYITPMFSFYKSIGELKMTQEEYALLTAIVILSPDRQYIKDREAVEKLQEPLLDVLQKLCKIHQPENPQHFACLLGRLTELRTFNHHHAEMLMSW  454
                                   253       263       273  ||   284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454
                                                          276|                                                                                                                                                                                
                                                           278                                                                                                                                                                                

Chain B from PDB  Type:PROTEIN  Length:208
                                                                                                                                                                                                                                                 
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh......hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhh.........hhhhhhhhhhhhhh..hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4wvd B  245 LTPDQQTLLHFIMDSYNKQRMPQEITNKILKEEFSAEENFLILTEMATNHVQVLVEFTKKLPGFQTLDHEDQIALLKGSAVEAMFLRSAEIFNKKLPSGHSDLLEERIRNSSDEYITPMFSFYKSIGELKMTQEEYALLTAIVILSPDRQYIKDREAVEKLQEPLLDVLQKLCKIHQPENPQHFACLLGRLTELRTFNHHHAEMLMSW  454
                                   254       264       274       284       294       304       314       324       334       344       354||     366       376       386       396       406       416       426       436       446        
                                                                                                                                        355|                                                                                                
                                                                                                                                         358                                                                                                

Chain C from PDB  Type:PROTEIN  Length:16
                                                 
               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
                4wvd C 2260 NLGLEDIIRKALMGSF 2275
                                  2269      

Chain D from PDB  Type:PROTEIN  Length:17
                                                  
               SCOP domains ----------------- SCOP domains
               CATH domains ----------------- CATH domains
               Pfam domains ----------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------- SAPs(SNPs)
                    PROSITE ----------------- PROSITE
                 Transcript ----------------- Transcript
                4wvd D 2259 SNLGLEDIIRKALMGSF 2275
                                  2268       

   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 4WVD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (100, 110)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        NCOR1_HUMAN | O753762eqr 3h52 3kmz 3n00 4mdd
        NR1H4_HUMAN | Q96RI11osh 1osk 3bej 3dct 3dcu 3fli 3fxv 3gd2 3hc5 3hc6 3l1b 3okh 3oki 3olf 3omk 3omm 3oof 3ook 3p88 3p89 3rut 3ruu 3rvf 4oiv 4qe6 4qe8 5iaw 5ick 5q0i 5q0j 5q0k 5q0l 5q0m 5q0n 5q0o 5q0p 5q0q 5q0r 5q0s 5q0t 5q0u 5q0v 5q0w 5q0x 5q0y 5q0z 5q10 5q11 5q12 5q13 5q14 5q15 5q16 5q17 5q18 5q19 5q1a 5q1b 5q1c 5q1d 5q1e 5q1f 5q1g 5q1h 5q1i

(-) Related Entries Specified in the PDB File

4ii6 4II6 CONTAINS THE SAME PROTEIN COMPLEXED WITH IVERMECTIN