Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) 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 :  2.30
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
19NA2Ligand/Ion(2S)-2-CYCLOHEXYL-2-[2-(2,6-DIMETHOXYPYRIDIN-3-YL)-5,6-DIFLUORO-1H-BENZIMIDAZOL-1-YL]-N-(TRANS-4-HYDROXYCYCLOHEXYL)ACETAMIDE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
19NA1Ligand/Ion(2S)-2-CYCLOHEXYL-2-[2-(2,6-DIMETHOXYPYRIDIN-3-YL)-5,6-DIFLUORO-1H-BENZIMIDAZOL-1-YL]-N-(TRANS-4-HYDROXYCYCLOHEXYL)ACETAMIDE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
19NA1Ligand/Ion(2S)-2-CYCLOHEXYL-2-[2-(2,6-DIMETHOXYPYRIDIN-3-YL)-5,6-DIFLUORO-1H-BENZIMIDAZOL-1-YL]-N-(TRANS-4-HYDROXYCYCLOHEXYL)ACETAMIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:273 , ILE A:277 , ASN A:287 , MET A:294 , PHE A:333 , SER A:336 , ILE A:339 , PHE A:340 , ILE A:361 , TYR A:373 , HOH A:605 , HOH A:624 , HOH A:632binding site for residue 9NA A 501
2AC2SOFTWAREILE C:273 , ILE C:277 , ASN C:287 , MET C:332 , PHE C:333 , SER C:336 , ILE C:339 , PHE C:340 , ILE C:356 , ILE C:361 , TYR C:373 , HIS C:451 , HOH C:603 , HOH C:630binding site for residue 9NA C 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5Q1C)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5Q1C)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5Q1C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5Q1C)

(-) Exons   (0, 0)

(no "Exon" information available for 5Q1C)

(-) 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:229
                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5q1c A 248 ELTPDQQTLLHFIMDSYNKQRMPQEITNKILKEAFSAEENFLILTEMATNHVQVLVEFTKKLPGFQTLDHEDQIALLKGSAVEAMFLRSAEIFNKKLPSGHSDLLEARIRNSGISDEYITPMFSFYKSIGELKMTQEEYALLTAIVILSPDRQYIKDREAVEKLQEPLLDVLQKLCKIHQPENPQHFACLLGRLTELRTFNHHHAEMLMSWRVNDHKFTPLLCEIWDVQ 476
                                   257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467         


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
                 5q1c B 746 HQLLRYLLDKD 756
                                   755 


Chain C from PDB  Type:PROTEIN  Length:228
                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5q1c C 248 ELTPDQQTLLHFIMDSYNKQRMPQEITNKILKEAFSAEENFLILTEMATNHVQVLVEFTKKLPGFQTLDHEDQIALLKGSAVEAMFLRSAEIFNKKLPSGHSDLLEARIRNSGISDEYITPMFSFYKSIGELKMTQEEYALLTAIVILSPDRQYIKDREAVEKLQEPLLDVLQKLCKIHQPENPQHFACLLGRLTELRTFNHHHAEMLMSWRVNDHKFTPLLCEIWDV 475
                                   257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467        


Chain D from PDB  Type:PROTEIN  Length:10
                                          
               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
                 5q1c D 746 HQLLRYLLDK 755
                                   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 5Q1C)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5Q1C)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5Q1C)

(-) Gene Ontology  (71, 75)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    9NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5q1c)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5q1c
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  A8K1V4_HUMAN | A8K1V4
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  NR1H4_HUMAN | Q96RI1
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  A8K1V4_HUMAN | A8K1V4
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  NR1H4_HUMAN | Q96RI1
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 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 5q0y 5q0z 5q10 5q11 5q12 5q13 5q14 5q15 5q16 5q18 5q19 5q1a 5q1b 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 5q0y 5q0z 5q10 5q11 5q12 5q13 5q14 5q15 5q16 5q17 5q18 5q19 5q1a 5q1b 5q1d 5q1e 5q1f 5q1g 5q1h 5q1i

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5Q1C)