Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE ATP-GATED P2X7 ION CHANNEL BOUND TO ALLOSTERIC ANTAGONIST GW791343
 
Authors :  A. Karasawa, T. Kawate
Date :  29 Nov 16  (Deposition) - 04 Jan 17  (Release) - 04 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.30
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Membrane Protein: Atp-Gated Ion Channel: Allosteric Antagonist Bound: Closed State, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Karasawa, T. Kawate
Structural Basis For Subtype-Specific Inhibition Of The P2X Receptor.
Elife V. 5 2016
PubMed-ID: 27935479  |  Reference-DOI: 10.7554/ELIFE.22153

(-) Compounds

Molecule 1 - P2X PURINOCEPTOR
    Chains: A
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Taxid: 7108
    Gene: P2RX7
    Organism Common: GIANT PANDA
    Organism Scientific: AILUROPODA MELANOLEUCA
    Organism Taxid: 9646
    Other Details: BOTH THE N- AND C-TERMINI ARE DISORDERED AND THE ELECTRON DENSITY WAS NOT WELL-DEFINED.

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (3x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
17RS1Ligand/IonN~2~-(3,4-DIFLUOROPHENYL)-N-{2-METHYL-5-[(PIPERAZIN-1-YL)METHYL]PHENYL}GLYCINAMIDE
2NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
17RS3Ligand/IonN~2~-(3,4-DIFLUOROPHENYL)-N-{2-METHYL-5-[(PIPERAZIN-1-YL)METHYL]PHENYL}GLYCINAMIDE
2NAG9Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:85 , PHE A:88 , ALA A:91 , ASP A:92 , TYR A:93 , THR A:94 , PHE A:95 , PHE A:103 , MET A:105 , PHE A:108 , LYS A:110 , GLN A:116 , TRP A:167 , TYR A:295 , TYR A:298 , GLU A:305binding site for residue 7RS A 404
2AC2SOFTWAREASN A:183 , SER A:184 , GLU A:186 , ASN A:187binding site for Mono-Saccharide NAG A 401 bound to ASN A 187
3AC3SOFTWAREASN A:202binding site for Mono-Saccharide NAG A 403 bound to ASN A 202
4AC4SOFTWAREASN A:213binding site for Mono-Saccharide NAG A 402 bound to ASN A 213

(-) SS Bonds  (5, 5)

Asymmetric Unit
No.Residues
1A:119 -A:168
2A:129 -A:152
3A:135 -A:162
4A:216 -A:226
5A:260 -A:269

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Cys A:168 -Pro A:169

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5U1Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5U1Y)

(-) Exons   (0, 0)

(no "Exon" information available for 5U1Y)

(-) 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:317
                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh..eeeee.eeeeeeeee..eeeeeeeee..eeeeeeeeehhhhhh......eeeeeeeeeeeeeeeeeeee................eeee......eeeeeeeeee..eeeeeeeeee.............hhhhhh.eeeeeeeeee....eeee.....................eeehhhhhhhh..hhhhhhhhheeeeeeeeeeee.........eeeeeee......hhhhh...eeeeeeeeee..eeeeeeeeeeeeeeeeeeeeeeeeehhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5u1y A  34 HALVFSYISFALISDKRYQKKEPLISSVHTKVKGIAEVKAEILENGMKKMVSGVFDTADYTFPLQGNSFFVMTNFIKTEGQQQGLCPDFPTARTICSSDRGCKKGRMDPQSKGIQTGRCVVYKERLKTCEVSAWCPIEEVKDAPRPALLNSAENFTVLIKNNIDFPGHNYTTRNILPGVNITCTFHKTQNPQCPIFRLGDIFQETGDSFSDVAIQGGIMGIEIYWDCNLDGWFHHCRPKYSFRRLDDKTTSESLYPGYNFRYAKYYKENNVEKRTLIKVFGIRFDILVFGTGGKFNVIQLAVYIGSVISYFGLATVF 350
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343
   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 5U1Y)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5U1Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5U1Y)

(-) Gene Ontology  (100, 100)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric 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
    7RS  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Cys A:168 - Pro A:169   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - 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
  5u1y
    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
  G1M6C4_AILME | G1M6C4
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
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
  G1M6C4_AILME | G1M6C4
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        G1M6C4_AILME | G1M6C4: 5u1l 5u1u 5u1v 5u1w 5u1x 5u2h

(-) Related Entries Specified in the PDB File

5u1l 5u1u 5u1v 5u1w 5u1x 5u2h