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 A52V/S54N/K66E VARIANT OF THE MURINE T CELL RECEPTOR V BETA 8.2 DOMAIN
 
Authors :  S. Cho, C. P. Swaminathan, J. Yang, M. C. Kerzic, R. Guan, M. C. Kieke, D. M R. A. Mariuzza, E. J. Sundberg
Date :  16 Aug 05  (Deposition) - 21 Mar 06  (Release) - 29 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  T Cell Receptor, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Cho, C. P. Swaminathan, J. Yang, M. C. Kerzic, R. Guan, M. C. Kieke, D. M. Kranz, R. A. Mariuzza, E. J. Sundberg
Structural Basis Of Affinity Maturation And Intramolecular Cooperativity In A Protein-Protein Interaction.
Structure V. 13 1775 2005
PubMed-ID: 16338399  |  Reference-DOI: 10.1016/J.STR.2005.08.015

(-) Compounds

Molecule 1 - T CELL RECEPTOR BETA CHAIN V
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PT7-7
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Common: NORWAY RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1MLA1Ligand/IonMALONIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:28 , ARG A:44 , ASP A:59 , GLY A:96 , THR A:99 , HOH A:221 , HOH A:256 , HOH A:297 , HOH A:316 , HOH A:347BINDING SITE FOR RESIDUE MLA A 200

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:23 -A:92

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ser A:7 -Pro A:8

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2APF)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2APF)

(-) Exons   (0, 0)

(no "Exon" information available for 2APF)

(-) 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:112
 aligned with A2NAI0_RAT | A2NAI0 from UniProtKB/TrEMBL  Length:95

    Alignment length:112
                             1                                                                                            95                
                             |       9        19        29        39        49        59        69        79        89     |   -         -  
           A2NAI0_RAT     - -MEAAVTQSPRNKVTVTGKNVTFNCHQTDNHNYMYWYRQDMGHGLRLIHYSYGSGSFENGDIPEGYKVSRPNQENFFLTLESASPSQTSVYFCASS----------------   -
               SCOP domains d2apfa_ A: automated matches                                                                                     SCOP domains
               CATH domains 2apfA00 A:-1-117 Immunoglobulins                                                                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee..eeeee....eeeeeee.....eeeeeee.....eeeeeee......ee.......eee.....eeeeee...hhhhheeeeeeee.....ee...eeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 2apf A  -1 ILEAAVTQSPRNKVAVTGEKVTLSCQQTNNHNNMYWYRQDTGHGLRLIHYSYGVGNTEKGDIPDGYEASRPSQEQFSLILELATPSQTTVYFCASGGGGTLYFGAGTRLSVL 117
                                     8        18        28        38        48        58    ||  69        79        89        99 ||    115  
                                                                                           63|                                 101|         
                                                                                            65                                  108         


Chain A from PDB  Type:PROTEIN  Length:112
 aligned with TVB5_MOUSE | P04213 from UniProtKB/Swiss-Prot  Length:122

    Alignment length:116
                                    16        26        36        46        56        66        76        86        96       106       116      
           TVB5_MOUSE     7 HMEAAVTQSPRSKVAVTGGKVTLSCHQTNNHDYMYWYRQDTGHGLRLIHYSYVADSTEKGDIPDGYKASRPSQENFSLILELASLSQTAVYFCASSGTGGALDTQYFGPGTRLLVL 122
               SCOP domains d2apfa_ A: automated matches                                                                                         SCOP domains
               CATH domains 2apfA00 A:-1-117 Immunoglobulins                                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee..eeeee....eeeeeee.....eeeeeee.....eeeeeee......ee.......eee.....eeeeee...hhhhheeeeeeee...----..ee...eeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 2apf A  -1 ILEAAVTQSPRNKVAVTGEKVTLSCQQTNNHNNMYWYRQDTGHGLRLIHYSYGVGNTEKGDIPDGYEASRPSQEQFSLILELATPSQTTVYFCASGGGG----TLYFGAGTRLSVL 117
                                     8        18        28        38        48        58    ||  69        79        89        |-   | ||111      
                                                                                           63|                               98   99 ||         
                                                                                            65                                     101|         
                                                                                                                                    108
   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  (1, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2APF)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2APF)

 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
    MLA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ser A:7 - Pro A:8   [ 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
  2apf
    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
  A2NAI0_RAT | A2NAI0
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
  TVB5_MOUSE | P04213
    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
  A2NAI0_RAT | A2NAI0
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  TVB5_MOUSE | P04213
    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
        TVB5_MOUSE | P04213: 1d9k 1lp9 1u3h 2apb 2apt 2apv 2apw 2apx 2aq1 2aq2 2aq3 2icw 2j8u 2uwe 4nhu
UniProtKB/TrEMBL
        A2NAI0_RAT | A2NAI0: 2apb 2apt 2apv 2apw 2apx

(-) Related Entries Specified in the PDB File

2apb THE G17E/S54N/L81S VARIANT OF THE MURINE T CELL RECEPTOR V BETA 8.2 DOMAIN
2apt THE G17E/S54N/K66E/Q72H/E80V/L81S/T87S/G96V VARIANT OF THE MURINE T CELL RECEPTOR V BETA 8.2 DOMAIN
2apv THE G17E/A52V/S54N/Q72H/E80V/L81S/T87S/G96V VARIANT OF THE MURINE T CELL RECEPTOR V BETA 8.2 DOMAIN
2apw THE G17E/A52V/S54N/K66E/E80V/L81S/T87S/G96V VARIANT OF THE MURINE T CELL RECEPTOR V BETA 8.2 DOMAIN
2apx THE G17E/A52V/S54N/K66E/Q72H/E80V/L81S/T87S/G96V VARIANT OF THE MURINE T CELL RECEPTOR V BETA 8.2 DOMAIN
2aq1 T-CELL RECEPTOR V BETA DOMAIN VARIANT (G17E/A52V/S54N/K66E/ E80V/L81S/T87S/G96V) COMPLEXED WITH SUPERANTIGEN SEC3 MUTANT
2aq2 T-CELL RECEPTOR V BETA DOMAIN VARIANT (G17E/A52V/S54N/K66E/ L81S) COMPLEXED WITH SUPERANTIGEN SEC3 MUTANT
2aq3 T-CELL RECEPTOR V BETA DOMAIN VARIANT (G17E/L81S) COMPLEXED WITH SUPERANTIGEN SEC3 MUTANT