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(-) Description

Title :  THE HUMAN P2Y1 RECEPTOR IN COMPLEX WITH MRS2500
 
Authors :  D. Zhang, Z. Gao, K. Jacobson, G. W. Han, R. Stevens, Q. Zhao, B. Wu
Date :  16 Jan 15  (Deposition) - 01 Apr 15  (Release) - 29 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  C  (1x)
Keywords :  Human P2Y1 Receptor, G Protein Coupled Receptor, Platelet Activation, Membrane Protein, Transport Protein, Psi-Biology (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Zhang, Z. G. Gao, K. Zhang, E. Kiselev, S. Crane, J. Wang, S. Paoletta C. Yi, L. Ma, W. Zhang, G. W. Han, H. Liu, V. Cherezov, V. Katritch, H. Jiang, R. C. Stevens, K. A. Jacobson, Q. Zhao, B. Wu
Two Disparate Ligand-Binding Sites In The Human P2Y1 Receptor
Nature V. 520 317 2015
PubMed-ID: 25822790  |  Reference-DOI: 10.1038/NATURE14287

(-) Compounds

Molecule 1 - P2Y PURINOCEPTOR 1,RUBREDOXIN,P2Y PURINOCEPTOR 1
    Chains: A, C
    Engineered: YES
    Expression System: SPODOPTERA
    Expression System Taxid: 7106
    Expression System Vector Type: BACULOVIRUS
    Gene: P2RY1
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS, CLOSTRIDIUM PASTEURIANUM
    Organism Taxid: 9606, 1501
    Other Details: CHIMERA PROTEIN OF P2Y PURINOCEPTOR 1 (P2RY1_HUMA) WITH RUBREDOXIN (RUBR_CLOPA) INSERTED INTO ICL3 DOMAIN BETWEEN RESIDUES 247LYS AND 253PRO, AND REPLACED RESIDUES 248ASN TO 252SER.
    Synonym: P2Y1, ATP RECEPTOR, PURINERGIC RECEPTOR, RD

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AC
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
12ID2Ligand/Ion[(1R,2S,4S,5S)-4-[2-IODO-6-(METHYLAMINO)-9H-PURIN-9-YL]-2-(PHOSPHONOOXY)BICYCLO[3.1.0]HEX-1-YL]METHYLDIHYDROGEN PHOSPHATE
2ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
12ID1Ligand/Ion[(1R,2S,4S,5S)-4-[2-IODO-6-(METHYLAMINO)-9H-PURIN-9-YL]-2-(PHOSPHONOOXY)BICYCLO[3.1.0]HEX-1-YL]METHYLDIHYDROGEN PHOSPHATE
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
12ID1Ligand/Ion[(1R,2S,4S,5S)-4-[2-IODO-6-(METHYLAMINO)-9H-PURIN-9-YL]-2-(PHOSPHONOOXY)BICYCLO[3.1.0]HEX-1-YL]METHYLDIHYDROGEN PHOSPHATE
2ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:42 , LEU A:44 , LYS A:46 , TYR A:110 , ARG A:195 , THR A:201 , TYR A:203 , ASP A:204 , THR A:205 , ASN A:283 , ALA A:286 , ARG A:287 , GLN A:291 , ASN A:299 , TYR A:303 , TYR A:306 , ARG A:310 , HOH A:1202 , HOH A:1205binding site for residue 2ID A 1101
2AC2SOFTWARECYS A:1006 , CYS A:1009 , CYS A:1039 , CYS A:1042binding site for residue ZN A 1102
3AC3SOFTWARELYS C:46 , TYR C:110 , ARG C:195 , THR C:201 , ASP C:204 , THR C:205 , ASN C:283 , ALA C:286 , ARG C:287 , GLN C:291 , ASN C:299 , TYR C:303 , TYR C:306 , ARG C:310binding site for residue 2ID C 1101
4AC4SOFTWARECYS C:1006 , CYS C:1009 , CYS C:1039 , CYS C:1042binding site for residue ZN C 1102

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:42 -A:296
2A:124 -A:202
3C:42 -C:296
4C:124 -C:202

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Lys A:81 -Pro A:82
2Lys C:81 -Pro C:82

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4XNW)

(-) 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:346
                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeee.....eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee.....ee.....hhhhh.....hhhhh...........hhh.eee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4xnw A   38 SSFKCALTKTGFQFYYLPAVYILVFIIGFLGNSVAIWMFVFHMKPWSGISVYMFNLALADFLYVLTLPALIFYYFNKTDWIFGDAMCKLQRFIFHVNLYGSILFLTCISAHRYSGVVYPLKSLGRLKKKNAICISVLVWLIVVVAISPILFYSGTGVRKNKTITCYDTTSDEYLRSYFIYSMCTTVAMFCVPLVLILGCYGLIVRALIYKMKKYTCTVCGYIYNPEDGDPDNGVNPGTDFKDIPDDWVCPLCGVGKDQFEEVEEPLRRKSIYLVIIVLTVFAVSYIPFHVMKTMNLRARLDFQTPAMCAFNDRVYATYQVTRGLASLNSCVNPILYFLAGDTFRRR  334
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247|     1010      1020      1030      1040      1050   ||  258       268       278       288       298       308       318       328      
                                                                                                                                                                                                                                           247|                                                 1054|                                                                                 
                                                                                                                                                                                                                                           1001                                                   253                                                                                 


Chain C from PDB  Type:PROTEIN  Length:350
                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeee.....eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee.....ee.....hhhhh.....hhhhh...........hhh.eee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4xnw C   38 SSFKCALTKTGFQFYYLPAVYILVFIIGFLGNSVAIWMFVFHMKPWSGISVYMFNLALADFLYVLTLPALIFYYFNKTDWIFGDAMCKLQRFIFHVNLYGSILFLTCISAHRYSGVVYPLKSLGRLKKKNAICISVLVWLIVVVAISPILFYSGTGVRKNKTITCYDTTSDEYLRSYFIYSMCTTVAMFCVPLVLILGCYGLIVRALIYKMKKYTCTVCGYIYNPEDGDPDNGVNPGTDFKDIPDDWVCPLCGVGKDQFEEVEEPLRRKSIYLVIIVLTVFAVSYIPFHVMKTMNLRARLDFQTPAMCAFNDRVYATYQVTRGLASLNSCVNPILYFLAGDTFRRRLSRA  338
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247|     1010      1020      1030      1040      1050   ||  258       268       278       288       298       308       318       328       338
                                                                                                                                                                                                                                           247|                                                 1054|                                                                                     
                                                                                                                                                                                                                                           1001                                                   253
   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 4XNW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (60, 60)

Asymmetric Unit(hide GO term definitions)

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  4xnw
    Family and Domain Information: ProDom | SYSTERS
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  P2RY1_HUMAN | P47900
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  RUBR_CLOPA | P00268
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 Related Entries

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

UniProtKB/Swiss-Prot
        P2RY1_HUMAN | P47900: 1y36 4xnv
        RUBR_CLOPA | P00268: 1b13 1b2j 1b2o 1be7 1bfy 1c09 1fhh 1fhm 1irn 1iro 1r0f 1r0g 1r0h 1r0i 1r0j 1smm 1smu 1smw 1t9o 1t9p 1t9q 2pve 4mbs 4rxn 4xnv 5rxn 5uiw 5vbl

(-) Related Entries Specified in the PDB File

4xnv RELATED ID: GPCR-86 RELATED DB: TARGETTRACK