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(-) Description

Title :  CRYSTAL STRUCTURE OF P2Y12 RECEPTOR IN COMPLEX WITH 2MESADP
 
Authors :  J. Zhang, K. Zhang, Z. G. Gao, S. Paoletta, D. Zhang, G. W. Han, T. Li, L. Ma C. E. Muller, H. Yang, H. Jiang, V. Cherezov, V. Katritch, K. A. Jacobso R. C. Stevens, B. Wu, Q. Zhao, Gpcr Network (Gpcr)
Date :  25 Mar 14  (Deposition) - 30 Apr 14  (Release) - 03 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Purinergic Receptor P2Y12, Agonist-Bound, G-Protein Coupled Receptor (Gpcr), Membrane Protein, Signaling Protein-Agonist Complex, Psi- Biology, Gpcr Network, Structural Genomics, Signaling Membrane Protein, Gpcr, Platelet Activation, Membrane (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Zhang, K. Zhang, Z. G. Gao, S. Paoletta, D. Zhang, G. W. Han, T. Li, L. Ma, W. Zhang, C. E. Muller, H. Yang, H. Jiang, V. Cherezov, V. Katritch, K. A. Jacobson, R. C. Stevens, B. Wu, Q. Zhao
Agonist-Bound Structure Of The Human P2Y12 Receptor
Nature V. 509 119 2014
PubMed-ID: 24784220  |  Reference-DOI: 10.1038/NATURE13288

(-) Compounds

Molecule 1 - P2Y PURINOCEPTOR 12, SOLUBLE CYTOCHROME B562
    Chains: A
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Plasmid: PFASTBAC1
    Expression System Strain: SF9
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIROUS
    Gene: HORK3, P2RY12, P2Y12, CYBC
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS, ESCHERICHIA COLI, HOMO SAPIENS
    Organism Taxid: 9606, 562, 9606
    Other Details: CHIMERA PROTEIN OF N-TERMINAL RESIDUES 2-223 FROM P2Y12R (P2Y12_HUMAN), SOLUBLE CYTOCHROME B562 (C562_ECOLX), AND C- TERMINAL RESIDUES 224-342 FROM P2Y12R (P2Y12_HUMAN).
    Synonym: P2Y12, ADP-GLUCOSE RECEPTOR, ADPG-R, P2T(AC), P2Y(AC), P2Y(CYC), P2Y12 PLATELET ADP RECEPTOR, P2Y(ADP), SP1999, CYTOCHROME B-562

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric/Biological Unit (4, 6)
No.NameCountTypeFull Name
16AD1Ligand/Ion2-(METHYLSULFANYL)ADENOSINE 5'-(TRIHYDROGENDIPHOSPHATE)
2CLR1Ligand/IonCHOLESTEROL
3OLC3Ligand/Ion(2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTADEC-9-ENOATE
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:93 , CYS A:97 , SER A:101 , VAL A:102 , TYR A:105 , SER A:156 , ASN A:159 , LYS A:174 , CYS A:175 , LYS A:179 , HIS A:187 , VAL A:190 , ASN A:191 , CYS A:194 , ARG A:256 , TYR A:259 , GLN A:263 , LYS A:280 , HOH A:1319 , HOH A:1322 , HOH A:1331 , HOH A:1336 , HOH A:1348BINDING SITE FOR RESIDUE 6AD A 1201
2AC2SOFTWARESER A:55 , ILE A:61 , LYS A:64 , ASN A:65 , ILE A:68 , TRP A:149 , PHE A:153BINDING SITE FOR RESIDUE CLR A 1202
3AC3SOFTWAREGLN A:98 , ILE A:161 , ASN A:164BINDING SITE FOR RESIDUE OLC A 1203
4AC4SOFTWAREARG A:231 , VAL A:236 , THR A:275 , TYR A:278 , SER A:282 , OLC A:1205BINDING SITE FOR RESIDUE OLC A 1204
5AC5SOFTWAREASP A:20 , ILE A:23 , LEU A:27 , SER A:282 , OLC A:1204BINDING SITE FOR RESIDUE OLC A 1205
6AC6SOFTWAREASN A:1022 , GLN A:1025 , GLN A:1041 , ARG A:1062 , HOH A:1315BINDING SITE FOR RESIDUE PEG A 1206

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:17 -A:270
2A:97 -A:175

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4PXZ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4PXZ)

(-) 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:392
                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4pxz A   15 SLCTRDYKITQVLFPLLYTVLFFVGLITNGLAMRIFFQIRSKSNFIIFLKNTVISDLLMILTFPFKILSDAKLGTGPLRTFVCQVTSVIFYFTMYISISFLGLITIDRYQKTTRPPKNLLGAKILSVVIWAFMFLLSLPNMILTNRQPRDKNVKKCSFLKSEFGLVWHEIVNYICQVIFWINFLIVIVCYTLITKELYRSYVRTADLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLRGVGKVPRKKVNVKVFIIIAVFFICFVPFHFARIPYTLSQTRDVFDCTAENTLFYVKESTLWLTSLNACLNPFIYFFLCKSF  305
                                    24        34        44        54        64        74        84        94       104       114       124    || 139       149       159       169       179       189       199       209       219   || 1006      1016      1026      1036      1046      1056      1066      1076      1086      1096      1106|      233       243       253       263       273       283       293       303  
                                                                                                                                            129|                                                                                     223|                                                                                                     1106|                                                                                 
                                                                                                                                             135                                                                                     1001                                                                                                       224
   Legend:   → Mismatch (orange background)
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  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 4PXZ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (48, 48)

Asymmetric/Biological Unit(hide GO term definitions)

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  4pxz
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  C562_ECOLX | P0ABE7
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  P2Y12_HUMAN | Q9H244
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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 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
        P2Y12_HUMAN | Q9H244: 1t78 1vz1 1y9c 4ntj 4py0

(-) Related Entries Specified in the PDB File

4ntj RELATED ID: GPCR-87 RELATED DB: TARGETTRACK
4py0