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

(-) Description

Title :  CRYSTAL STRUCTURE OF THE ANTI-PRION FAB 3F4 IN COMPLEX WITH ITS PEPTIDE EPITOPE
 
Authors :  Z. F. Kanyo, K. M. Pan, R. A. Williamson, D. R. Burton, S. B. Prusiner, R. J. Fletterick, F. E. Cohen
Date :  20 Aug 99  (Deposition) - 17 Apr 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  H,L,P
Keywords :  Immunoglobulin Fold, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. F. Kanyo, K. M. Pan, R. A. Williamson, D. R. Burton, S. B. Prusiner, R. J. Fletterick, F. E. Cohen
Antibody Binding Defines A Structure For An Epitope That Participates In The Prpc-->Prpsc Conformational Change.
J. Mol. Biol. V. 293 855 1999
PubMed-ID: 10543972  |  Reference-DOI: 10.1006/JMBI.1999.3193
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FAB LIGHT CHAIN
    Chains: L
    Fragment: FAB ANTIBODY 3F4, LIGHT CHAIN
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: ANTI-PRION FAB 3F4
 
Molecule 2 - FAB HEAVY CHAIN
    Chains: H
    Fragment: FAB ANTIBODY 3F4, HEAVY CHAIN
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: ANTI-PRION FAB 3F4
 
Molecule 3 - RECOGNITION PEPTIDE
    Chains: P
    Engineered: YES
    Other Details: SEQUENCE COORESPONDING TO AA104-113 OF SYRIAN HAMSTER PRION PROTEIN
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : HLP

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1CU4)

(-) Sites  (0, 0)

(no "Site" information available for 1CU4)

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:92
2H:137 -H:192
3L:23 -L:88
4L:134 -L:194

(-) Cis Peptide Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1Thr L:7 -Pro L:8
2Phe L:94 -Pro L:95
3Tyr L:140 -Pro L:141
4Phe H:143 -Pro H:144
5Glu H:145 -Pro H:146
6Trp H:185 -Pro H:186
7Ala P:104 -Pro P:105

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1CU4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1CU4)

(-) Exons   (0, 0)

(no "Exon" information available for 1CU4)

(-) 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:215
                                                                                                                                                                                                                                                        
               SCOP domains d1cu4h1 H:3-110 Immunoglobulin heavy chain variable domain, VH                                                  d1cu4h2 H:111-213 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                         SCOP domains
               CATH domains 1cu4H01 H:3-110 Immunoglobulins                                                                                 1cu4H02 H:111-209 Immunoglobulins                                                                  ---- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...eee.....eeeeeee.........eeeeee.....eeeeeeeehhhheeee.hhhh..eeeeee....eeeeee........eeeeeeehhhhee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eeeeeeeee..eeeeeeeeeee.hhhhhh.eeeeeeehhhheeeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1cu4 H    3 KLQQSGAELVRSGASVKLSCTASGFNIKDYYIQWVKQRPEQGLEWIGWIDPENGNSEYAPRFQGKATMTADTLSNTAYLQLSSLTSEDTAVYYCNADLHDYWGQGTTLTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRVTS  213
                                    12        22        32        42        52|       61        71        81 |||    88        98       108       118       128       138       148       158       168       178       188       198       208     
                                                                            52A                            82A||                                                                                                                                   
                                                                                                            82B|                                                                                                                                   
                                                                                                             82C                                                                                                                                   


Chain L from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                            
               SCOP domains d1cu4l1 L:1-106A Immunoglobulin light chain kappa variable domain, VL-kappa                                     d1cu4l2 L:108-214 Immunoglobulin light chain kappa constant domain, CL-kappa                                SCOP domains
               CATH domains 1cu4L01 L:1-108 Immunoglobulins                                                                                  1cu4L02 L:109-214 Immunoglobulins                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhhh.eeeeeeee..eeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1cu4 L    1 DVVMTQTPLSLSVTIGQPASISCKSSQSLLDSDGKTYLIWVFQRPGQSPKRLIFLVSKRDSGVPDRFTGSGSGTDFTLKISRVEAEDVGVYYCWQGTHFPHTVGGGTKLEIARADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  214
                                    10        20       27C||      35        45        55        65        75        85        95| ||   105 ||    115       125       135       145       155       165       175       185       195       205         
                                                     27A||||                                                                  95A ||    106A|                                                                                                          
                                                      27B|||                                                                     97|      108                                                                                                          
                                                       27C||                                                                      99                                                                                                                   
                                                        27D|                                                                                                                                                                                           
                                                         27E                                                                                                                                                                                           


Chain P from PDB  Type:PROTEIN  Length:10
                                           
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .......... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                1cu4 P  104 APKTNMKHMA  113
                                   113
   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 1CU4)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1CU4)

 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 1cu4)
 
  Sites
(no "Sites" information available for 1cu4)
 
  Cis Peptide Bonds
    Ala P:104 - Pro P:105   [ RasMol ]  
    Glu H:145 - Pro H:146   [ RasMol ]  
    Phe H:143 - Pro H:144   [ RasMol ]  
    Phe L:94 - Pro L:95   [ RasMol ]  
    Thr L:7 - Pro L:8   [ RasMol ]  
    Trp H:185 - Pro H:186   [ RasMol ]  
    Tyr L:140 - Pro L:141   [ 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
  1cu4
    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 1CU4)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1CU4)