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(-) Description

Title :  HUMAN SIGMA-1 RECEPTOR BOUND TO 4-IBP
 
Authors :  H. R. Schmidt, S. Zheng, E. G. Gurpinar, A. Koehl, A. Manglik, A. C. Kruse
Date :  13 Jan 16  (Deposition) - 06 Apr 16  (Release) - 11 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Sigma-1 Receptor, Transmembrane Receptor, Ligand, Trimer, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. R. Schmidt, S. Zheng, E. Gurpinar, A. Koehl, A. Manglik, A. C. Kruse
Crystal Structure Of The Human Sigma 1 Receptor.
Nature V. 532 527 2016
PubMed-ID: 27042935  |  Reference-DOI: 10.1038/NATURE17391

(-) Compounds

Molecule 1 - SIGMA NON-OPIOID INTRACELLULAR RECEPTOR 1
    Chains: A, B, C
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: SF9
    Expression System Plasmid: PFASTBAC1
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Gene: SIGMAR1, OPRS1, SRBP, AAG8
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: AGING-ASSOCIATED GENE 8 PROTEIN,SR31747-BINDING PROTEIN,SR- BP,SIGMA 1-TYPE OPIOID RECEPTOR,HSIGMAR1

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 22)

Asymmetric/Biological Unit (3, 22)
No.NameCountTypeFull Name
161V3Ligand/IonN-(1-BENZYLPIPERIDIN-4-YL)-4-IODOBENZAMIDE
2OLC7Ligand/Ion(2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTADEC-9-ENOATE
3SO412Ligand/IonSULFATE ION

(-) Sites  (22, 22)

Asymmetric Unit (22, 22)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREVAL A:84 , MET A:93 , PHE A:107 , SER A:117 , TYR A:120 , ASP A:126 , GLU A:172 , TYR A:206binding site for residue 61V A 301
02AC2SOFTWAREARG A:204 , ARG A:208 , ARG A:211binding site for residue SO4 A 302
03AC3SOFTWAREPHE A:37 , GLN A:38 , ARG A:39 , ARG A:175binding site for residue SO4 A 303
04AC4SOFTWARELEU A:52 , ASP A:53 , HIS A:54 , SER A:130 , ASN A:167binding site for residue SO4 A 304
05AC5SOFTWAREVAL B:78 , TRP B:83 , MET B:87 , PHE B:101 , TYR B:114 , ASP B:120 , GLU B:166 , LEU B:176 , ALA B:179 , TYR B:200binding site for residue 61V B 301
06AC6SOFTWAREARG B:202 , ARG B:205 , SO4 B:305binding site for residue SO4 B 302
07AC7SOFTWARETYR B:195 , ARG B:198 , SO4 B:305binding site for residue SO4 B 303
08AC8SOFTWAREARG A:114 , ARG B:108 , ARG C:114binding site for residue SO4 B 304
09AC9SOFTWAREPHE B:194 , ARG B:198 , SO4 B:302 , SO4 B:303binding site for residue SO4 B 305
10AD1SOFTWAREGLU B:207 , TRP C:27binding site for residue OLC B 306
11AD2SOFTWARETRP B:23 , GLN B:27 , TRP C:27binding site for residue OLC B 307
12AD3SOFTWARELEU B:94 , SER B:95 , GLY B:170 , OLC B:309binding site for residue OLC B 308
13AD4SOFTWARETRP B:115 , GLU B:117 , GLY B:170 , OLC B:308binding site for residue OLC B 309
14AD5SOFTWAREGLU B:49 , LEU B:73 , TRP B:75binding site for residue OLC B 310
15AD6SOFTWAREVAL C:84 , TRP C:89 , MET C:93 , PHE C:107 , SER C:117 , TYR C:120 , ILE C:124 , ASP C:126 , GLU C:172 , THR C:181 , ALA C:185 , TYR C:206binding site for residue 61V C 301
16AD7SOFTWAREGLU C:78 , ARG C:208 , ARG C:211binding site for residue SO4 C 302
17AD8SOFTWAREGLN C:38 , ARG C:39 , ARG C:175binding site for residue SO4 C 303
18AD9SOFTWAREASP C:53 , HIS C:54 , ASN C:167binding site for residue SO4 C 304
19AE1SOFTWARESER B:124 , GLY B:125 , PRO B:142 , ARG C:60binding site for residue SO4 C 305
20AE2SOFTWAREARG C:204binding site for residue SO4 C 306
21AE3SOFTWARETHR B:209 , TRP C:121 , ALA C:122 , GLU C:123 , ARG C:175 , GLY C:176binding site for residue OLC C 307
22AE4SOFTWAREGLU B:144binding site for residue OLC C 308

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5HK2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5HK2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5HK2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5HK2)

(-) Exons   (0, 0)

(no "Exon" information available for 5HK2)

(-) 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:217
                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.....hhhhh.eeeeee..eeeeeeeeee...eeeeeeee...eeee.....eeeeeeeee..eeeee......eee....eeee.....eeeee...eeeeeeeee.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hk2 A   2 QWAVGRRWAWAALLLAVAAVLTQVVWLWLGTQSFVFQREEIAQLARQYAGLDHELAFSRLIVELRRLHPGHVLPDEELQWVFVNAGGWMGAMCLLHASLSEYVLLFGTALGSRGHSGRYWAEISDTIISGTFHQWREGTTKSEVFYPGETVVHGPGEATAVEWGPNTWMVEYGRGVIPSTLAFALADTVFSTQDFLTLFYTLRSYARGLRLELTTYL 218
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       


Chain B from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhh.......hhhhhhhhh....hhhhhhhhhhhhhhhhh.....hhhhh..eeeee..eeeeeeeeee...eeeeeeee...eeee.....eeeeeeeee..eeeee......eee....eeee.....eeeee...eeeeeeeeehhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hk2 B   3 WAVGRLLLAVAAVLTQVVWLWLGTQSFVFQREEIAQLARQYAGLDHELAFSRLIVELRRLHPGHVLPDEELQWVFVNAGGWMGAMCLLHASLSEYVLLFGTALGSRGHSGRYWAEISDTIISGTFHQWREGTTKSEVFYPGETVVHGPGEATAVEWGPNTWMVEYGRGVIPSTLAFALADTVFSTQDFLTLFYTLRSYARGLRLELTTYLFG 214
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212  


Chain C from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh....hhhhhhhhhhhhhhhhh.....hhhhh..eeeee..eeeeeeeeee...eeeeeeee...eeee.....eeeeeeeee..eeeee......eee....eeee.....eeeee...eeeeeeeeehhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hk2 C   8 RWAWAALLLAVAAVLTQVVWLWLGTQSFVFQREEIAQLARQYAGLDHELAFSRLIVELRRLHPGHVLPDEELQWVFVNAGGWMGAMCLLHASLSEYVLLFGTALGSRGHSGRYWAEISDTIISGTFHQWREGTTKSEVFYPGETVVHGPGEATAVEWGPNTWMVEYGRGVIPSTLAFALADTVFSTQDFLTLFYTLRSYARGLRLELTTYLF 219
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217
   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 5HK2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5HK2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5HK2)

(-) Gene Ontology  (25, 25)

Asymmetric/Biological Unit(hide GO term definitions)

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  5hk2
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        SGMR1_HUMAN | Q99720: 5hk1

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