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 :  PLEUROBRACHIA BACHEI IGLUR3 LBD GLYCINE COMPLEX
 
Authors :  R. J. Grey, M. L. Mayer
Date :  17 Apr 15  (Deposition) - 21 Oct 15  (Release) - 18 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Membrane Protein, Glutamate Receptor, Ion Channel (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Alberstein, R. Grey, A. Zimmet, D. K. Simmons, M. L. Mayer
Glycine Activated Ion Channel Subunits Encoded By Ctenophor Glutamate Receptor Genes.
Proc. Natl. Acad. Sci. Usa V. 112 E6048 2015
PubMed-ID: 26460032  |  Reference-DOI: 10.1073/PNAS.1513771112

(-) Compounds

Molecule 1 - GLUTAMATE RECEPTOR KAINATE-LIKE PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22
    Expression System Strain: ORIGAMI B(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PBIGLUR3
    Organism Common: SEA GOOSEBERRY
    Organism Scientific: PLEUROBRACHIA BACHEI
    Organism Taxid: 34499
    Other Details: THE CONSTRUCT CONTAINS RESIDUES N399-D519 AND D660- N795 OF THE PBIGLUR3 LIGAND BINDING DOMAIN CONNECTED BY A SYNTHETIC GT LINKER, WITH AN E399N MUTATION OF THE NATIVE SEQUENCE INTRODUCED TO FACILITATE REMOVAL OF THE AFFINITY PURIFICATION TAG.
    Synonym: PBIGLUR3

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1GLY1Mod. Amino AcidGLYCINE
2NA2Ligand/IonSODIUM ION
3SO42Ligand/IonSULFATE ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1GLY2Mod. Amino AcidGLYCINE
2NA-1Ligand/IonSODIUM ION
3SO44Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:66 , ALA A:94 , LEU A:95 , SER A:96 , ARG A:101 , ARG A:147 , ASN A:148 , GLU A:191 , HOH A:598binding site for residue GLY A 301
2AC2SOFTWARETYR A:161 , PHE A:212 , GLN A:213 , HOH A:596 , HOH A:657binding site for residue SO4 A 302
3AC3SOFTWAREHIS A:9 , ARG A:11 , ARG A:32 , ASN A:57 , LYS A:87binding site for residue SO4 A 303
4AC4SOFTWAREASP A:145 , GLU A:150 , LYS A:170 , HOH A:698binding site for residue NA A 304
5AC5SOFTWAREASP A:160 , HOH A:660binding site for residue NA A 305

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:28 -A:36

(-) Cis Peptide Bonds  (2, 3)

Asymmetric Unit
No.Residues
1Met A:18 -Pro A:19
2Ile A:192 -Pro A:193

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ZDM)

(-) 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:250
                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee...................hhhhh.hhhhhhhhhhhhhhheeeeee............hhhhhhhhh....eeeeeee.hhhhhh..ee....eeeeeeeeee.......hhhhhhhh...eeeee..hhhhhhhhhh.hhhhhhhhhhheee.hhhhhhhhhhh..eeeeeeehhhhhhh.....eee....eeeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zdm A   2 SNNLNGMHLRLGIIPEMPFISEPSLGCTNIRDPSCYTGVNVEIVSMMSQDLNFTYNFITPEDLKFGGKEWNGLIRDLLDNKTDMIVVALSNNAVRKADIDFSLSMMDGGLGALVKSDGTDLSHPLELLNQDKYQWGVVDSRNPELLLASNQNADYNRIAEDAVKVGSYGEGLERMRAGGFVFIDEIPGINYATKGECDIVQIGETFQPFELAFGLRKNSPFKNLVDTFMLGIREQGVISELYAKYENQKG 301
                                    11        21        31        41        51        61       |76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       301
                                                                                              69|                                                                                                                                                                                 255|
                                                                                               75                                                                                                                                                                                  301
   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 4ZDM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

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
    GLY  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ile A:192 - Pro A:193   [ RasMol ]  
    Met A:18 - Pro A:19   [ 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
  4zdm
    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
  H6S0J1_PLEBA | H6S0J1
    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
  H6S0J1_PLEBA | H6S0J1
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 4ZDM)

(-) Related Entries Specified in the PDB File

4yki 4ykj 4ykk 4ykp