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

(-) Description

Title :  CRYSTAL STRUCTURE OF FAB HGR-2 F6, A COMPETITIVE ANTAGONIST OF THE GLUCAGON RECEPTOR
 
Authors :  L. M. Wright, A. M. Brzozowski, R. E. Hubbard, A. C. W. Pike, S. M. Roberts, R. N. Skovgaard, I. Svendsen, H. Vissing, R. P. Bywater
Date :  04 Jan 00  (Deposition) - 10 May 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  H,L
Keywords :  Glucagon Receptor, Monoclonal Antibody, Fab, Receptor Antagonist, Typical Immunoglobulin Fold, Light Chain, Heavy Chain, Antigen Binding Site, Complementarity-Determining Regions, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. M. Wright, A. M. Brzozowski, R. E. Hubbard, A. C. Pike, S. M. Roberts, R. N. Skovgaard, I. Svendsen, H. Vissing, R. P. Bywater
Structure Of Fab Hgr-2 F6, A Competitive Antagonist Of The Glucagon Receptor.
Acta Crystallogr. , Sect. D V. 56 573 2000
PubMed-ID: 10771426  |  Reference-DOI: 10.1107/S090744490000233X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FAB HGR-2 F6
    Chains: L
    Fragment: LIGHT CHAIN
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: USING RBF MICE, MONOCLONAL ANTIBODIES WERE GENERATED AGAINST THE INTACT HUMAN MEMBRANE-BOUND GLUCAGON RECEPTOR. FAB FRAGMENTS WERE PRODUCED FROM THE INTACT IGG MONOCLONAL ANTIBODY BY PAPAIN DIGESTION. FINAL PURIFICATION OF THE FAB FRAGMENTS WAS PERFORMED USING BOTH A MONOQ ION EXCHANGE COLUMN AND SUBSEQUENTLY A MONOS COLUMN.
 
Molecule 2 - FAB HGR-2 F6
    Chains: H
    Fragment: HEAVY CHAIN
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: USING RBF MICE, MONOCLONAL ANTIBODIES WERE GENERATED AGAINST THE INTACT HUMAN MEMBRANE-BOUND GLUCAGON RECEPTOR. FAB FRAGMENTS WERE PRODUCED FROM THE INTACT IGG MONOCLONAL ANTIBODY BY PAPAIN DIGESTION. FINAL PURIFICATION OF THE FAB FRAGMENTS WAS PERFORMED USING BOTH A MONOQ ION EXCHANGE COLUMN AND SUBSEQUENTLY A MONOS COLUMN.

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : HL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1DQD)

(-) Sites  (0, 0)

(no "Site" information available for 1DQD)

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:95
2H:149 -H:204
3L:23 -L:87
4L:133 -L:193

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Ser L:7 -Pro L:8
2Tyr L:93 -Pro L:94
3Tyr L:139 -Pro L:140
4Phe H:155 -Pro H:156
5Glu H:157 -Pro H:158
6Trp H:197 -Pro H:198

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1DQD)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1DQD)

(-) Exons   (0, 0)

(no "Exon" information available for 1DQD)

(-) 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 H from PDB  Type:PROTEIN  Length:221
                                                                                                                                                                                                                                                             
               SCOP domains d1dqdh1 H:1-122 Immunoglobulin heavy chain variable domain, VH                                                            d1dqdh2 H:123-222 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                     SCOP domains
               CATH domains 1dqdH01 H:1-122 Immunoglobulins                                                                                           1dqdH02 H:123-220 Immunoglobulins                                                                -- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee.......eeeeeee.....eeeeeeee....eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeeeee........eeee...eeeee........eeeee.........eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dqd H   1 EVQLQESGPSLVKPSQTLSLTCSVTGDSITSGYWNWIRKFPGNKLEYMGYISYSGSTYYNPSLKSRLSITRDTSRNQYYLQLKSVTPEDTATYYCASPPGYYGSGPYAMDYWGQGTSVTVSSAKTTPPSVYPLAPGSAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKISPG 222
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       141       151       161       171       181       191       201       211       221 
                                                                                                                                                                   138|                                                                                  
                                                                                                                                                                    140                                                                                  


Chain L from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains d1dqdl1 L:1-106 Immunoglobulin light chain kappa variable domain, VL-kappa                                d1dqdl2 L:107-214 Immunoglobulin light chain kappa constant domain, CL-kappa                                 SCOP domains
               CATH domains 1dqdL01 L:1-107 Immunoglobulins                                                                            1dqdL02 L:108-209 Immunoglobulins                                                                     ----- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee....hhhhh.eeeeeeeeeee.....eeeeee...ee...eeeee.........eeeeeeeeeehhhhh...eeeeeee........eeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dqd L   1 DIVLSQSPAIMSASPGEKVTITCSASSSVSYMHWFQQKPGTSPKLCIYTTSNLASGVPARFSGSGSGTSYSLTISRMEAEDAATYYCQQRSTYPPTFGSGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPRDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNECA 214
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
   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  (4, 4)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1DQD)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1DQD)

 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
(no "Ligands, Modified Residues, Ions" information available for 1dqd)
 
  Sites
(no "Sites" information available for 1dqd)
 
  Cis Peptide Bonds
    Glu H:157 - Pro H:158   [ RasMol ]  
    Phe H:155 - Pro H:156   [ RasMol ]  
    Ser L:7 - Pro L:8   [ RasMol ]  
    Trp H:197 - Pro H:198   [ RasMol ]  
    Tyr L:139 - Pro L:140   [ RasMol ]  
    Tyr L:93 - Pro L:94   [ 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 ](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
  1dqd
    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
  (no 'UniProt ID/Accession number' available) |
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProt
 
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
  (no 'UniProt ID/Accession number' available) |
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 1DQD)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1DQD)