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(-) Description

Title :  THE CRYSTAL STRUCTURE OF NOCICEPTIN/ORPHANIN FQ PEPTIDE RECEPTOR (NOP) IN COMPLEX WITH SB-612111 (PSI COMMUNITY TARGET)
 
Authors :  R. L. Miller, A. A. Thompson, C. Trapella, R. Guerrini, D. Malfacini, N. G. W. Han, V. Cherezov, G. Calo, V. Katritch, R. C. Stevens, Gpcr Netwo
Date :  31 Aug 15  (Deposition) - 21 Oct 15  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A (1x),B (1x)
Keywords :  Nociceptin/Orphanin Fq Peptide Receptor, Nop, Orl-1, N/Ofq, Opioid Receptor, G Protein-Coupled Receptor, Gpcr, Membrane Protein, Lipidic Cubic Phase, Bret, Receptor-Ligand Conformational Pair, Structural Genomics, Psi-Biology, Gpcr Network, Signaling Protein, Psicnt-127 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. L. Miller, A. A. Thompson, C. Trapella, R. Guerrini, D. Malfacini, N. Patel, G. W. Han, V. Cherezov, G. Calo, V. Katritch, R. C. Stevens
The Importance Of Ligand-Receptor Conformational Pairs In Stabilization: Spotlight On The N/Ofq G Protein-Coupled Receptor.
Structure V. 23 2291 2015
PubMed-ID: 26526853  |  Reference-DOI: 10.1016/J.STR.2015.07.024

(-) Compounds

Molecule 1 - SOLUBLE CYTOCHROME B562,NOCICEPTIN RECEPTOR
    Chains: A, B
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: SF9
    Expression System Plasmid: PFASTBAC
    Expression System Strain: SF9
    Expression System Taxid: 7108
    Expression System Vector Type: PLASMID
    Gene: CYBC, OPRL1, OOR, ORL1
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: ESCHERICHIA COLI, HOMO SAPIENS
    Organism Taxid: 562, 9606
    Synonym: CYTOCHROME B-562,KAPPA-TYPE 3 OPIOID RECEPTOR,KOR-3,ORPHANIN FQ RECEPTOR

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (1x): A (1x)B (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
1DGW2Ligand/Ion(5S,7S)-7-{[4-(2,6-DICHLOROPHENYL)PIPERIDIN-1-YL]METHYL}-1-METHYL-6,7,8,9-TETRAHYDRO-5H-BENZO[7]ANNULEN-5-OL
2OLA7Ligand/IonOLEIC ACID
3OLC1Ligand/Ion(2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTADEC-9-ENOATE
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1DGW1Ligand/Ion(5S,7S)-7-{[4-(2,6-DICHLOROPHENYL)PIPERIDIN-1-YL]METHYL}-1-METHYL-6,7,8,9-TETRAHYDRO-5H-BENZO[7]ANNULEN-5-OL
2OLA5Ligand/IonOLEIC ACID
3OLC-1Ligand/Ion(2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTADEC-9-ENOATE
Biological Unit 2 (3, 4)
No.NameCountTypeFull Name
1DGW1Ligand/Ion(5S,7S)-7-{[4-(2,6-DICHLOROPHENYL)PIPERIDIN-1-YL]METHYL}-1-METHYL-6,7,8,9-TETRAHYDRO-5H-BENZO[7]ANNULEN-5-OL
2OLA2Ligand/IonOLEIC ACID
3OLC1Ligand/Ion(2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTADEC-9-ENOATE
Biological Unit 3 (2, 6)
No.NameCountTypeFull Name
1DGW1Ligand/Ion(5S,7S)-7-{[4-(2,6-DICHLOROPHENYL)PIPERIDIN-1-YL]METHYL}-1-METHYL-6,7,8,9-TETRAHYDRO-5H-BENZO[7]ANNULEN-5-OL
2OLA5Ligand/IonOLEIC ACID
3OLC-1Ligand/Ion(2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTADEC-9-ENOATE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:89 , ASP A:147 , VAL B:1354binding site for residue OLA A 1201
02AC2SOFTWAREALA A:121 , LYS A:124 , OLA A:1204binding site for residue OLA A 1202
03AC3SOFTWAREVAL A:55 , PRO A:105 , THR A:109 , PHE A:115binding site for residue OLA A 1203
04AC4SOFTWARELYS A:124 , OLA A:1202 , ARG B:1304binding site for residue OLA A 1204
05AC5SOFTWAREPHE A:91 , TRP A:175binding site for residue OLA A 1205
06AC6SOFTWAREGLN A:107 , ASP A:110 , ILE A:127 , ASP A:130 , TYR A:131 , ILE A:219 , VAL A:279 , GLN A:280 , VAL A:283 , TYR A:309binding site for residue DGW A 1206
07AC7SOFTWARELEU A:67 , PRO B:1181 , PHE B:1182binding site for residue OLA B 1501
08AC8SOFTWAREARG A:240 , LYS B:1188binding site for residue OLA B 1502
09AC9SOFTWAREGLN B:1171 , ASP B:1194 , TYR B:1195 , MET B:1198 , ILE B:1283 , SER B:1287 , TRP B:1340 , GLN B:1344 , THR B:1369 , TYR B:1373binding site for residue DGW B 1503
10AD1SOFTWARELEU A:288 , VAL A:290 , TYR B:1153 , ALA B:1207 , ASP B:1211 , VAL B:1225 , LYS B:1230binding site for residue OLC B 1504

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:123 -A:200
2B:1187 -B:1264

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Thr A:206 -Pro A:207
2Thr B:1270 -Pro B:1271

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5DHH)

(-) 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:282
                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhheeeee....eeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5dhh A   45 FLPLGLKVTIVGLYLAVCVGGLLGNCLVMYVILRHTKMKTATNIYIFNLALADTLVLLTLPFQGTDILLGFWPFGNALCKTVIAIDYYNMFTSTFTLTAMSVDRYVAICHPRTSSKAQAVNVAIWALASVVGVPVAIMGSAQVEDEEIECLVEIPTPQDYWGPVFAICIFLFSFIVPVLVISVCYSLMIRRLRGVRLLSGSREKDRNLRRITRLVLVVVAVFVGCWTPVQVFVLAQGLGVQPSSETAVAILRFCTALGYVNSCLNPILYAFLDENFKACFRK  332
                                    54        64        74        84        94       104       114       124       134       144       154||     170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330  
                                                                                                                                        155|                                                                                                                                                                          
                                                                                                                                         162                                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:387
                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhee........ee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5dhh B 1003 LEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLAFLPLGLKVTIVGLYLAVCVGGLLGNCLVMYVILRHTKMKTATNIYIFNLALADTLVLLTLPFQGTDILLGFWPFGNALCKTVIAIDYYNMFTSTFTLTAMSVDRYVAICHPIRALDVRTSSKAQAVNVAIWALASVVGVPVAIMGSAQVEEIECLVEIPTPQDYWGPVFAICIFLFSFIVPVLVISVCYSLMIRRLRGSREKDRNLRRITRLVLVVVAVFVGCWTPVQVFVLAQGLGVQPSSETAVAILRFCTALGYVNSCLNPILYAFLDENFKACFRKFC 1398
                                  1012      1022      1032      1042      1052      1062      1072      1082      1092      1102   || 1113      1123      1133      1143      1153      1163      1173      1183      1193      1203      1213      1223      1233      1243      1253   || 1265      1275      1285      1295      1305  ||  1321      1331      1341      1351      1361      1371      1381      1391       
                                                                                                                                1106|                                                                                                                                                 1257|                                            1308|                                                                                   
                                                                                                                                 1108                                                                                                                                                  1260                                             1315
   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 5DHH)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (43, 49)

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 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 4n6h 4nc3 4ntj 4o9r 4or2 4pxz 4py0 4qim 4qin 4rwa 4rwd 4u9d 4u9e 4yay 4z34 4z35 4z36 4zud 5awi 5bu7 5dhg 5iu4 5iu7 5iu8 5iua 5iub 5jtb 5k2a 5k2b 5k2c 5k2d 5l31 5l32 5l7d 5l7i 5ndd 5ndz 5nj6 5tvn 5uen 5uig 5unf 5ung 5unh 5uvi
        OPRX_HUMAN | P41146: 4ea3 5dhg

(-) Related Entries Specified in the PDB File

4ea3 NOP IN COMPLEX WITH C24 LIGAND. RELATED ID: GPCR-79 RELATED DB: TARGETTRACK