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

(-) Description

Title :  MNEMIOPSIS LEIDYI ML032222A IGLUR LBD COMPLEX WITH ALANINE
 
Authors :  R. G. Alberstein, M. L. Mayer
Date :  04 Mar 15  (Deposition) - 21 Oct 15  (Release) - 18 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A,B
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 - ML032222A IGLUR
    Chains: A, B
    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
    Fragment: LIGAND BINDING DOMAIN
    Gene: ML032222A
    Organism Scientific: MNEMIOPSIS LEIDYI
    Organism Taxid: 27923
    Other Details: THE CONSTRUCT CONTAINS RESIDUES K409-E526 AND T682- S815 OF THE ML032222A LIGAND BINDING DOMAIN CONNECTED BY A SYNTHETIC GT LINKER

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1ALA2Mod. Amino AcidALANINE
2GLY2Mod. Amino AcidGLYCINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:17 , PHE A:63 , ASP A:91 , LEU A:92 , SER A:93 , ARG A:98 , ARG A:144 , HIS A:145 , GLU A:188 , TYR A:214 , GLY A:302binding site for residue ALA A 301
2AC2SOFTWAREPHE A:63 , ASP A:91 , LEU A:92 , SER A:93 , ARG A:98 , HIS A:145 , GLU A:188 , ALA A:301binding site for residue GLY A 302
3AC3SOFTWAREGLU B:17 , PHE B:63 , ASP B:91 , LEU B:92 , SER B:93 , ARG B:98 , ARG B:144 , HIS B:145 , GLU B:188 , TYR B:214 , GLY B:302binding site for residue ALA B 301
4AC4SOFTWAREPHE B:63 , ASP B:91 , LEU B:92 , SER B:93 , ARG B:98 , HIS B:145 , GLU B:188 , TYR B:214 , ALA B:301binding site for residue GLY B 302

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:28 -A:33
2B:28 -B:33
3B:200 -B:255

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Gln A:18 -Pro A:19
2Ser A:250 -Gly A:251
3Gln B:18 -Pro B:19

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YKJ)

(-) 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:249
                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee........ee.....hhhh.eehhhhhhhhhhhhhhh.eeeee.........ee....eehhhhhhhhh....eeeeeee.hhhhhh..ee....eeeeeeeeee.......hhhhhhhh...eeeee..hhhhhhhhhh..hhhhhhhhhheee.hhhhhhhhhhh..eeeeeehhhhhhhh.....eee....eeeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ykj A   5 LIGRHLRLGSVEEQPFMFFATEGCEGNDCWSGMVNDMVVKLSEDLGFTYEYIQPDDRKFGALNKTTNEWNGMIRDLLDDKTDMIAIDLSTNSARKSAIDYSFPFMDAGIKAVVKGEGTTLNQVLELLDQDKYKWGVIGSRHPETLLKTHRDSRYSRLVDEGVELKDLNHAIETLRGGLFVFIDEGPVLAHNLISDCDVFSVGEEFQSFEYAFGLPKDSPYKSLIDSHLLKFREEGFIDILWEKWSSGAG 302
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244      || 
                                                                                                                                                                                                                                                                                251| 
                                                                                                                                                                                                                                                                                 301 


Chain B from PDB  Type:PROTEIN  Length:257
                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee........ee.....hhhh.eehhhhhhhhhhhhhhh.eeeee.................hhhhhhhhh....eeeeeee.hhhhhhhhee....eeeeeeeeee.......hhhhhhhh...eeeee..hhhhhhhhhh..hhhhhhhhhheee.hhhhhhhhhhh..eeeeeehhhhhhhh.....eee....eeeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ykj B   1 GSKNLIGRHLRLGSVEEQPFMFFATEGCEGNDCWSGMVNDMVVKLSEDLGFTYEYIQPDDRKFGALNKTTNEWNGMIRDLLDDKTDMIAIDLSTNSARKSAIDYSFPFMDAGIKAVVKGEGTTLNQVLELLDQDKYKWGVIGSRHPETLLKTHRDSRYSRLVDEGVELKDLNHAIETLRGGLFVFIDEGPVLAHNLISDCDVFSVGEEFQSFEYAFGLPKDSPYKSLIDSHLLKFREEGFIDILWEKWSSGNSVCAG 302
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250    || 
                                                                                                                                                                                                                                                                                        255| 
                                                                                                                                                                                                                                                                                         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 4YKJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4YKJ)

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    ALA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GLY  [ 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
    Gln A:18 - Pro A:19   [ RasMol ]  
    Gln B:18 - Pro B:19   [ RasMol ]  
    Ser A:250 - Gly A:251   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - 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
  4ykj
    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
  A0A0R4I973_M | A0A0R4I973
    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
  A0A0R4I973_M | A0A0R4I973
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        A0A0R4I973_M | A0A0R4I973: 4yki 4ykk 4ykp 5cmb 5cmc

(-) Related Entries Specified in the PDB File

4yki 4ykk 4ykp 4ykv