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(-) Description

Title :  LIGAND BINDING TO FARNESOID-X-RECEPTOR
 
Authors :  C. Joseph, A. Alker, D. Banner, J. Benz, D. Burger, M. Hennig, A. Ruf, G. S M. Stihle, R. Thoma, M. Rudolph, R. E. Martin, B. Kuhn, C. Shao, H. Yang, S. K. Burley
Date :  31 May 17  (Deposition) - 05 Jul 17  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  D3R, Fxr, Docking, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Joseph, A. Alker, D. Banner, J. Benz, D. Burger, M. Hennig, A. Ruf, G. Schoch, M. Stihle, R. Thoma, M. Rudolph, R. E. Martin, B. Kuhn
Ligand Binding To Farnesoid-X-Receptor
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - BILE ACID RECEPTOR
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NR1H4, BAR, FXR, HRR1, RIP14
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: FARNESOID 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
 
Molecule 2 - COACTIVATOR PEPTIDE SRC-1 HD3
    Chains: B, D
    Engineered: YES
    Fragment: UNP RESIDUES 744-757
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
19LY2Ligand/Ion(2S)-N,2-DICYCLOHEXYL-2-{5,6-DIFLUORO-2-[6-(1H-PYRAZOL-1-YL)PYRIDIN-3-YL]-1H-BENZIMIDAZOL-1-YL}ACETAMIDE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
19LY1Ligand/Ion(2S)-N,2-DICYCLOHEXYL-2-{5,6-DIFLUORO-2-[6-(1H-PYRAZOL-1-YL)PYRIDIN-3-YL]-1H-BENZIMIDAZOL-1-YL}ACETAMIDE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
19LY1Ligand/Ion(2S)-N,2-DICYCLOHEXYL-2-{5,6-DIFLUORO-2-[6-(1H-PYRAZOL-1-YL)PYRIDIN-3-YL]-1H-BENZIMIDAZOL-1-YL}ACETAMIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:273 , THR A:274 , ILE A:277 , ASN A:287 , LEU A:291 , MET A:294 , HIS A:298 , MET A:332 , PHE A:333 , SER A:336 , ILE A:339 , PHE A:340 , ILE A:356 , SER A:359 , ILE A:361 , TYR A:373 , MET A:454 , LEU A:455binding site for residue 9LY A 501
2AC2SOFTWAREILE C:273 , THR C:274 , ILE C:277 , ASN C:287 , LEU C:291 , MET C:294 , HIS C:298 , PHE C:333 , SER C:336 , ILE C:339 , PHE C:340 , ILE C:356 , SER C:359 , ILE C:361 , TYR C:373 , MET C:454 , LEU C:455 , TRP C:458binding site for residue 9LY C 501

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:436 -C:436

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5Q0Y)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5Q0Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5Q0Y)

(-) Exons   (0, 0)

(no "Exon" information available for 5Q0Y)

(-) 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:230
                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5q0y A 247 MELTPDQQTLLHFIMDSYNKQRMPQEITNKILKEAFSAEENFLILTEMATNHVQVLVEFTKKLPGFQTLDHEDQIALLKGSAVEAMFLRSAEIFNKKLPSGHSDLLEARIRNSGISDEYITPMFSFYKSIGELKMTQEEYALLTAIVILSPDRQYIKDREAVEKLQEPLLDVLQKLCKIHQPENPQHFACLLGRLTELRTFNHHHAEMLMSWRVNDHKFTPLLCEIWDVQ 476
                                   256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476


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
                 5q0y B 745 DHQLLRYLLDK 755
                                   754 


Chain C from PDB  Type:PROTEIN  Length:230
                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5q0y C 247 MELTPDQQTLLHFIMDSYNKQRMPQEITNKILKEAFSAEENFLILTEMATNHVQVLVEFTKKLPGFQTLDHEDQIALLKGSAVEAMFLRSAEIFNKKLPSGHSDLLEARIRNSGISDEYITPMFSFYKSIGELKMTQEEYALLTAIVILSPDRQYIKDREAVEKLQEPLLDVLQKLCKIHQPENPQHFACLLGRLTELRTFNHHHAEMLMSWRVNDHKFTPLLCEIWDVQ 476
                                   256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476


Chain D 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
                 5q0y D 746 HQLLRYLLDKD 756
                                   755
   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 5Q0Y)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5Q0Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5Q0Y)

(-) Gene Ontology  (71, 75)

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 Related Entries

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

UniProtKB/Swiss-Prot
        A8K1V4_HUMAN | A8K1V4: 3p88 3p89 5q0j 5q0k 5q0l 5q0m 5q0n 5q0o 5q0p 5q0q 5q0r 5q0s 5q0t 5q0u 5q0v 5q0w 5q0x 5q0z 5q10 5q11 5q12 5q13 5q14 5q15 5q16 5q18 5q19 5q1a 5q1b 5q1c 5q1d 5q1e 5q1f 5q1g 5q1h 5q1i
        NR1H4_HUMAN | Q96RI1: 1osh 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 4wvd 5iaw 5ick 5q0i 5q0j 5q0k 5q0l 5q0m 5q0n 5q0o 5q0p 5q0q 5q0r 5q0s 5q0t 5q0u 5q0v 5q0w 5q0x 5q0z 5q10 5q11 5q12 5q13 5q14 5q15 5q16 5q17 5q18 5q19 5q1a 5q1b 5q1c 5q1d 5q1e 5q1f 5q1g 5q1h 5q1i

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