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

(-) Description

Title :  CRYSTAL STRUCTURE OF THE HUMAN OX2 OREXIN RECEPTOR BOUND TO THE INSOMNIA DRUG SUVOREXANT
 
Authors :  J. Yin, P. Kolb, J. C. Mobarec, D. M. Rosenbaum
Date :  06 Jan 15  (Deposition) - 14 Jan 15  (Release) - 25 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  G Protein-Coupled Receptor, Orexin Neurotransmitters, Orexin Receptor, Orexin-A, Orexin-B, Suvorexant, N-Linked Glycosylation, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Yin, J. C. Mobarec, P. Kolb, D. M. Rosenbaum
Crystal Structure Of The Human Ox2 Orexin Receptor Bound To The Insomnia Drug Suvorexant.
Nature V. 519 247 2015
PubMed-ID: 25533960  |  Reference-DOI: 10.1038/NATURE14035

(-) Compounds

Molecule 1 - HUMAN OREXIN RECEPTOR TYPE 2 FUSION PROTEIN TO P. ABYSII GLYCOGEN SYNTHASE
    Chains: A
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Plasmid: PFASTBAC1
    Expression System Taxid: 7108
    Expression System Vector Type: FASTBAC BACULOVIRUS
    Fragment: UNP O43614 RESIDUES 3-254, 294-388, AND UNP Q9V2J8 RESIDUES 218-413
    Gene: HCRTR2, PAB2292, PYRAB00770
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS, PYROCOCCUS ABYSSI GE5
    Organism Taxid: 9606, 272844
    Synonym: OX-2-R, OX2-R, OX2R, HYPOCRETIN RECEPTOR TYPE 2, GLYCOGEN SYNTHASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1OLA1Ligand/IonOLEIC ACID
2SUV1Ligand/Ion[(7R)-4-(5-CHLORO-1,3-BENZOXAZOL-2-YL)-7-METHYL-1,4-DIAZEPAN-1-YL][5-METHYL-2-(2H-1,2,3-TRIAZOL-2-YL)PHENYL]METHANONE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:111 , VAL A:114 , TRP A:120 , ILE A:130 , PRO A:131 , GLN A:134 , THR A:135 , GLN A:187 , GLU A:212 , ILE A:320 , ASN A:324 , HOH A:4025BINDING SITE FOR RESIDUE SUV A 2001

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:127 -A:210

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Pro A:50 -Lys A:51

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4S0V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4S0V)

(-) Exons   (0, 0)

(no "Exon" information available for 4S0V)

(-) 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:478
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhheeeeee.....eeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhh..hhhhhhhhhhhhhh....eeeee.........hhhhhhhhhhhhhhhhhhh.eeeeee...hhhhhhhhhhhhhhh..eeee....hhhhhhhhhh...eeee.......hhhhhhhhh...eeeee...hhhhhh.....eee...hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4s0v A   50 PKEYEWVLIAGYIIVFVVALIGNVLVCVAVWKNHHMRTVTNYFIVNLSLADVLVTITCLPATLVVDITETWFFGQSLCKVIPYLQTVSVSVSVLTLSCIALDRWYAICHPSTAKRARNSIVIIWIVSCIIMIPQAIVMECSTVFKTTLFTVCDERWGGEIYPKMYHICFFLVTYMAPLCLMVLAYLQIFRKLWCRQGIDCSFWNESYLTGSRDERKKSLLSKFGMDEGVTFMFIGRFDRGQKGVDVLLKAIEILSSKKEFQEMRFIIIGKGDPELEGWARSLEEKHGNVKVITEMLSREFVRELYGSVDFVIIPSYFEPFGLVALEAMCLGAIPIASAVGGLRDIITNETGILVKAGDPGELANAILKALELSRSDLSKFRENCKKRAMSFSKQIRARRKTARMLMVVLLVFAICYLPISILNVLKRVFGMFAHDRETVYAWFTFSHWLVYANSAANPIIYNFLSGKFREEFKAAFSC  381
                                    59        69        79        89        99       109       119       129       139       149       159|      173       183       193   ||  208       218       228       238       248     |1004      1014      1024      1034      1044      1054      1064      1074      1084      1094      1104      1114      1124      1134      1144      1154      1164      1174      1184      1194 ||    301       311       321       331   ||  343       353       363       373        
                                                                                                                                       159|                              197|                                                254|                                                                                                                                                                                               1196|                                      335|                                           
                                                                                                                                        164                               203                                                1001                                                                                                                                                                                                 294                                       338
   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 4S0V)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4S0V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4S0V)

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    OLA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SUV  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Pro A:50 - Lys A:51   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites 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
  4s0v
    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
  OX2R_HUMAN | O43614
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  Q9V2J8_PYRAB | Q9V2J8
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
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
  OX2R_HUMAN | O43614
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  Q9V2J8_PYRAB | Q9V2J8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q9V2J8_PYRAB | Q9V2J8: 2bfw 2bis 3fro 3l01 4zj8 4zjc 5u09

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4S0V)