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 :  CRYSTAL STRUCTURE OF THE EXTRACELLULAR DOMAIN OF HUMAN GABA(B) RECEPTOR GBR2
 
Authors :  Y. Geng, D. Xiong, L. Mosyak, D. L. Malito, J. Kniazeff, Y. Chen, S. Burma M. Quick, M. Bush, J. A. Javitch, J. -P. Pin, Q. R. Fan
Date :  05 May 12  (Deposition) - 06 Jun 12  (Release) - 15 Aug 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.02
Chains :  Asym./Biol. Unit :  A
Keywords :  Venus Flytrap Module, G-Protein Coupled Receptor, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Geng, D. Xiong, L. Mosyak, D. L. Malito, J. Kniazeff, Y. Chen, S. Burmakina, M. Quick, M. Bush, J. A. Javitch, J. P. Pin, Q. R. Fan
Structure And Functional Interaction Of The Extracellular Domain Of Human Gaba(B) Receptor Gbr2.
Nat. Neurosci. V. 15 970 2012
PubMed-ID: 22660477  |  Reference-DOI: 10.1038/NN.3133

(-) Compounds

Molecule 1 - GAMMA-AMINOBUTYRIC ACID TYPE B RECEPTOR SUBUNIT 2
    Chains: A
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Strain: SF9
    Expression System Taxid: 7108
    Fragment: EXTRACELLULAR DOMAIN, UNP RESIDUES 42-466'
    Gene: GABBR2, GPR51, GPRC3B
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: GABA-B RECEPTOR 2, GABA-B-R2, GABA-BR2, GABABR2, GB2, G- PROTEIN COUPLED RECEPTOR 51, HG20

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1FUC1Ligand/IonALPHA-L-FUCOSE
2NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:87 , ASN A:90 , LYS A:333BINDING SITE FOR RESIDUE NAG A 801
2AC2SOFTWAREASN A:389BINDING SITE FOR RESIDUE NAG A 802
3AC3SOFTWAREASN A:404 , NAG A:804 , FUC A:805BINDING SITE FOR RESIDUE NAG A 803
4AC4SOFTWARENAG A:803BINDING SITE FOR RESIDUE NAG A 804
5AC5SOFTWAREASN A:407 , NAG A:803BINDING SITE FOR RESIDUE FUC A 805
6AC6SOFTWARELYS A:112 , LYS A:115 , GLU A:450 , ASN A:453BINDING SITE FOR RESIDUE NAG A 806

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:108 -A:135
2A:237 -A:266
3A:265 -A:302

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Arg A:95 -Pro A:96

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4F12)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4F12)

(-) Exons   (0, 0)

(no "Exon" information available for 4F12)

(-) 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:410
                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeee.......hhhhhhhhhhhhhhhhhhhhhh......eeeeeeee...hhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhhh.eeee....hhhhhh......eee...hhhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhhhh.....eeeeeeee...hhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhh.......eeeee............hhhhhhhhhh..eeeee..............hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh...hhhhhhhhhhhhhh.eeee..eeeeee..ee..eeeeeeee..eeeeeeeee....eeee............... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f12 A  49 PPPSSPPLSIMGLMPLTKEVAKGSIGRGVLPAVELAIEQIRNESLLRPYFLDLRLYDTECDNAKGLKAFYDAIKYGPNHLMVFGGVCPSVTSIIAESLQGWNLVQLSFAATTPVLADKKKYPYFFRTVPSDNAVNPAILKLLKHYQWKRVGTLTQDVQRFSEVRNDLTGVLYGEDIEISDTESFSNDPCTSVKKLKGNDVRIILGQFDQNMAAKVFCCAYEENMYGSKYQWIIPGWYEPSWWEQVCLRKNLLAAMEGYIGVDFEPLSSKQIKTISGKTPQQYEREYNNKRSGVGPSKFHGYAYDGIWVIAKTLQRAMETLHASSRHQRIQDFNYTDHTLGRIILNAMNETNFFGVTGQVVFRNGERMGTIKFTQFQDSREVKVGEYNAVADTLEIINDTIRFQGSEPPKD 466
                                    58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288    || 306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466
                                                                                                                                                                                                                                                                              293|                                                                                                                                                                    
                                                                                                                                                                                                                                                                               302
   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 4F12)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4F12)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4F12)

(-) Gene Ontology  (19, 19)

Asymmetric/Biological Unit(hide GO term definitions)

 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
    FUC  [ 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 ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Arg A:95 - Pro A:96   [ 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
  4f12
    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
  GABR2_HUMAN | O75899
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
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
  GABR2_HUMAN | O75899
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        GABR2_HUMAN | O75899: 4f11 4mqe 4mqf 4mr7 4mr8 4mr9 4mrm 4ms1 4ms3 4ms4 4pas

(-) Related Entries Specified in the PDB File

4f11 THE SAME PROTEIN IN A DIFFERENT CRYSTAL FORM