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 :  1.8 A STRUCTURE OF THE HUMAN DELTA OPIOID 7TM RECEPTOR (PSI COMMUNITY TARGET)
 
Authors :  G. Fenalti, P. M. Giguere, V. Katritch, X. -P. Huang, A. A. Thompson, G. W V. Cherezov, B. L. Roth, R. C. Stevens, Gpcr Network (Gpcr)
Date :  12 Oct 13  (Deposition) - 25 Dec 13  (Release) - 05 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Human Opioid Receptor, Sodium Regulation, Allostery, Functional Selectivity, Gpcr Signaling, Constitutive Activity, Gpcr Network, Membrane Protein, Psi-Biology, Structural Genomics, Gpcr, Membrane, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Fenalti, P. M. Giguere, V. Katritch, X. P. Huang, A. A. Thompson, V. Cherezov, B. L. Roth, R. C. Stevens
Molecular Control Of Delta-Opioid Receptor Signalling.
Nature V. 506 191 2014
PubMed-ID: 24413399  |  Reference-DOI: 10.1038/NATURE12944

(-) Compounds

Molecule 1 - SOLUBLE CYTOCHROME B562, DELTA-TYPE OPIOID RECEPTOR CHIMERIC PROTEIN
    Chains: A
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Plasmid: PFASTBAC
    Expression System Strain: SF9
    Expression System Taxid: 7108
    Fragment: UNP P0ABE7 RESIDUES 23-128, UNP P41143 RESIDUES 36-338
    Gene: OPRD, OPRD1
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: ESCHERICHIA COLI, HOMO SAPIENS
    Organism Taxid: 562, 9606
    Synonym: D-OR-1, DOR-1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 23)

Asymmetric/Biological Unit (6, 23)
No.NameCountTypeFull Name
1EJ41Ligand/Ion(4BS,8R,8AS,14BR)-7-(CYCLOPROPYLMETHYL)-5,6,7,8,14,14B-HEXAHYDRO-4,8-METHANO[1]BENZOFURO[2,3-A]PYRIDO[4,3-B]CARBAZOLE-1,8A(9H)-DIOL
2NA1Ligand/IonSODIUM ION
3OLA12Ligand/IonOLEIC ACID
4OLC5Ligand/Ion(2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTADEC-9-ENOATE
5PGE3Ligand/IonTRIETHYLENE GLYCOL
6TLA1Ligand/IonL(+)-TARTARIC ACID

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRO A:115 , PHE A:116 , GLU A:1081 , OLA A:1217BINDING SITE FOR RESIDUE OLA A 1201
02AC2SOFTWARESER A:100 , OLC A:1212BINDING SITE FOR RESIDUE OLA A 1202
03AC3SOFTWAREASP A:288BINDING SITE FOR RESIDUE OLA A 1203
04AC4SOFTWAREILE A:279 , ILE A:289 , ASP A:290 , OLA A:1210BINDING SITE FOR RESIDUE OLA A 1204
05AC5SOFTWARETYR A:233 , ARG A:261 , OLA A:1215BINDING SITE FOR RESIDUE OLA A 1205
06AC6SOFTWARETYR A:87 , ASP A:145 , PHE A:159 , THR A:161 , OLA A:1209 , HOH A:1365BINDING SITE FOR RESIDUE OLA A 1206
07AC7SOFTWAREPHE A:137 , MET A:141 , CYS A:171 , ILE A:172BINDING SITE FOR RESIDUE OLC A 1207
08AC8SOFTWAREVAL A:185 , GLN A:201BINDING SITE FOR RESIDUE OLC A 1208
09AC9SOFTWAREALA A:54 , LEU A:55 , OLA A:1206 , PGE A:1214BINDING SITE FOR RESIDUE OLA A 1209
10BC1SOFTWAREASP A:293 , LEU A:295 , VAL A:296 , OLA A:1204BINDING SITE FOR RESIDUE OLA A 1210
11BC2SOFTWAREALA A:47BINDING SITE FOR RESIDUE OLA A 1211
12BC3SOFTWAREGLU A:118 , LYS A:166 , OLA A:1202 , OLC A:1222 , OLC A:1223 , HOH A:1391BINDING SITE FOR RESIDUE OLC A 1212
13BC4SOFTWAREOLA A:1209BINDING SITE FOR RESIDUE PGE A 1214
14BC5SOFTWAREVAL A:272 , OLA A:1205BINDING SITE FOR RESIDUE OLA A 1215
15BC6SOFTWAREARG A:261 , VAL A:316 , PHE A:320BINDING SITE FOR RESIDUE OLA A 1216
16BC7SOFTWAREPRO A:115 , PHE A:116 , OLA A:1201BINDING SITE FOR RESIDUE OLA A 1217
17BC8SOFTWARETHR A:82 , ALA A:83 , THR A:84 , ARG A:146 , ARG A:160 , ILE A:259 , HOH A:1328 , HOH A:1340BINDING SITE FOR RESIDUE TLA A 1218
18BC9SOFTWAREASP A:128 , TYR A:129 , MET A:132 , LYS A:214 , VAL A:217 , TRP A:274 , VAL A:281 , TRP A:284 , ILE A:304 , GLY A:307 , TYR A:308 , HOH A:1312 , HOH A:1316 , HOH A:1324 , HOH A:1336BINDING SITE FOR RESIDUE EJ4 A 1219
19CC1SOFTWAREASP A:95 , ASN A:131 , SER A:135 , HOH A:1307 , HOH A:1308BINDING SITE FOR RESIDUE NA A 1220
20CC2SOFTWARELYS A:81 , ILE A:86 , PHE A:89 , LYS A:166 , ASN A:169 , TRP A:173 , SER A:177 , MET A:184 , OLC A:1212BINDING SITE FOR RESIDUE OLC A 1222
21CC3SOFTWARELYS A:122 , TYR A:130 , LEU A:167 , ILE A:170 , MET A:184 , VAL A:185 , OLC A:1212 , HOH A:1366BINDING SITE FOR RESIDUE OLC A 1223

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:121 -A:198

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ser A:204 -Pro A:205

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4N6H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4N6H)

(-) Exons   (0, 0)

(no "Exon" information available for 4N6H)

(-) 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:408
                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh..hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeeeee..eeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4n6h A 1002 DLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLGSPGARSASSLALAIAITALYSAVCAVGLLGNVLVMFGIVRYTKMKTATNIYIFNLALADALATSTLPFQSAKYLMETWPFGELLCKAVLSIDYYNMFTSIFTLTMMSVDRYIAVCHPVKALDFRTPAKAKLINICIWVLASGVGVPIMVMAVTRPRDGAVVCMLQFPSPSWYWDTVTKICVFLFAFVVPILIITVCYGLMLLRLRSVRLLSGSKEKDRSLRRITRMVLVVVGAFVVCWAPIHIFVIVWTLVDIDRRDPLVVAALHLCIALGYANSSLNPVLYAFLDENFKRCFRQLCRKPCG  338
                                  1011      1021      1031      1041      1051      1061      1071      1081      1091      1101    ||  40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330        
                                                                                                                                 1106|                                                                                                                                                                                                                                                                                                              
                                                                                                                                    36
   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 4N6H)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4N6H)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4N6H)

(-) Gene Ontology  (48, 48)

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
    EJ4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    OLA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    OLC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PGE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    TLA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
    BC7  [ RasMol ]  +environment [ RasMol ]
    BC8  [ RasMol ]  +environment [ RasMol ]
    BC9  [ RasMol ]  +environment [ RasMol ]
    CC1  [ RasMol ]  +environment [ RasMol ]
    CC2  [ RasMol ]  +environment [ RasMol ]
    CC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ser A:204 - Pro A:205   [ 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
  4n6h
    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
  C562_ECOLX | P0ABE7
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  OPRD_HUMAN | P41143
    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
  C562_ECOLX | P0ABE7
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  OPRD_HUMAN | P41143
    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
        C562_ECOLX | P0ABE7: 1apc 1lm3 1m6t 1qpu 1qq3 256b 2bc5 2qla 3c62 3c63 3de8 3de9 3foo 3fop 3hni 3hnj 3hnk 3hnl 3iq5 3iq6 3l1m 3m15 3m4b 3m4c 3m79 3nmi 3nmj 3nmk 3tol 3tom 3u8p 4ea3 4eiy 4iaq 4iar 4ib4 4je9 4jea 4jeb 4jkv 4l6r 4nc3 4ntj 4o9r 4or2 4pxz 4py0 4qim 4qin 4rwa 4rwd 4u9d 4u9e 4yay 4z34 4z35 4z36 4zud 5awi 5bu7 5dhg 5dhh 5iu4 5iu7 5iu8 5iua 5iub 5jtb 5k2a 5k2b 5k2c 5k2d 5l31 5l32 5l7d 5l7i 5ndd 5ndz 5nj6 5tvn 5uen 5uig 5unf 5ung 5unh 5uvi
        OPRD_HUMAN | P41143: 1ozc 2iqm 4rwa 4rwd

(-) Related Entries Specified in the PDB File

4ej4 STRUCTURE OF THE DELTA-OPIOID RECEPTOR BOUND TO NALTRINDOLE. RELATED ID: GPCR-39 RELATED DB: TARGETTRACK