Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  THE CRYSTAL STRUCTURE OF THE 5C.C7 TCR
 
Authors :  L. K. Ely, E. W. Newell, M. M. Davis, K. C. Garcia
Date :  28 Jan 11  (Deposition) - 27 Apr 11  (Release) - 10 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Immunoglobulin Domain, T Cell Receptor, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. W. Newell, L. K. Ely, A. C. Kruse, P. A. Reay, S. N. Rodriguez, A. E. Lin M. S. Kuhns, K. C. Garcia, M. M. Davis
Structural Basis Of Specificity And Cross-Reactivity In T Cell Receptors Specific For Cytochrome C-I-E(K).
J. Immunol. V. 186 5823 2011
PubMed-ID: 21490152  |  Reference-DOI: 10.4049/JIMMUNOL.1100197

(-) Compounds

Molecule 1 - 5C.C7 ALPHA CHAIN
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - 5C.C7 BETA CHAIN
    Chains: B, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3QJH)

(-) Sites  (0, 0)

(no "Site" information available for 3QJH)

(-) SS Bonds  (12, 12)

Asymmetric Unit
No.Residues
1A:22 -A:90
2A:139 -A:189
3A:164 -B:174
4B:23 -B:92
5B:69 -B:75
6B:148 -B:213
7C:22 -C:90
8C:139 -C:189
9C:164 -D:174
10D:23 -D:92
11D:69 -D:75
12D:148 -D:213

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Ser A:6 -Pro A:7
2Thr B:7 -Pro B:8
3Tyr B:154 -Pro B:155
4Ser C:6 -Pro C:7
5Thr D:7 -Pro D:8
6Tyr D:154 -Pro D:155

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3QJH)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3QJH)

(-) Exons   (0, 0)

(no "Exon" information available for 3QJH)

(-) Sequences/Alignments

Asymmetric 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:195
                                                                                                                                                                                                                                   
               SCOP domains d3qjha1 A:1-117 automated matches                                                                           d3qjha2 A:118-206 automated matches                                                     SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee..eeeee....eeeeee....eeeeeeeee....eeeeeee..eeeee..eeeeee....eeeeee...hhhhheeeeeeeee.....eee...eeeeee........eeeeee.....eeeeee...............eee...eeeeehhhheeeeeeeeee.....hhhhhh............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qjh A   1 DQVEQSPSALSLHEGTGSALRCNFTTTMRAVQWFRKNRGSLINLFYLASGTKENGRLKSAFDSKERYSTLHIRDAQLEDSGTYFCAAEASNTNKVVFGTGTRLQVLPNIQNPDPAVYQLRDSKDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPS 206
                                    10        20        30      ||41        51        61        71||      85        95   ||  109       119       129  ||   141       151       161       171       181       191       201     
                                                               37|                               72|                    99|                         132|                                                                       
                                                                39                                77                    104                          135                                                                       


Chain B from PDB  Type:PROTEIN  Length:243
                                                                                                                                                                                                                                                                                   
               SCOP domains d3qjhb1 B:2-119 automated matches                                                                                  d3qjhb2 B:120-247 automated matches                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee..eeeee....eeeeee......eeeeeee.....eeeeeeee..eeeeehhhhhhheeee......eeeee...hhhhheeeeeeee........ee...eeeeee.hhhhh...eeeee..hhhhhhhhheeeeeeeeeee....eeeeeee..eee...eee....ee.........eeeeeeeeeehhhhh....eeeeeeee..................eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qjh B   2 MKVIQTPRYLVKGQGQKAKMRCIPEKGHPVVFWYQQNKNNEFKFLINFQNQEVLQQIDMTEKRFSAECPSNSPCSLEIQSSEAGDSALYLCASSLNNANSDYTFGSGTRLLVIEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD 247
                                    11        21        31        41        51        61        71        81        91       101       111   ||  124       134       144       154       164       174       184       194       204       214       224       234       244   
                                                                                                                                           115|                                                                                                                                
                                                                                                                                            119                                                                                                                                


Chain C from PDB  Type:PROTEIN  Length:195
                                                                                                                                                                                                                                   
               SCOP domains d3qjhc1 C:1-117 automated matches                                                                           d3qjhc2 C:118-206 automated matches                                                     SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee..eeeee....eeeeee....eeeeeeeee....eeeeeee...eeee..eeeeee....eeeeee...hhhhheeeeeeeee.....eee...eeeeee........eeeeee.....eeeeee...............eee...eeeeehhhheeeeeeeeee.....hhhhhh............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qjh C   1 DQVEQSPSALSLHEGTGSALRCNFTTTMRAVQWFRKNRGSLINLFYLASGTKENGRLKSAFDSKERYSTLHIRDAQLEDSGTYFCAAEASNTNKVVFGTGTRLQVLPNIQNPDPAVYQLRDSKDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPS 206
                                    10        20        30      ||41        51        61        71||      85        95   ||  109       119       129  ||   141       151       161       171       181       191       201     
                                                               37|                               72|                    99|                         132|                                                                       
                                                                39                                77                    104                          135                                                                       


Chain D from PDB  Type:PROTEIN  Length:242
                                                                                                                                                                                                                                                                                  
               SCOP domains d3qjhd1 D:2-119 automated matches                                                                                  d3qjhd2 D:120-246 automated matches                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee..eeeee....eeeeee......eeeeeee.....eeeeeeee..eeeeehhhhhhheeee......eeeee...hhhhheeeeeeee........ee...eeeeee.hhhhh...eeeee..hhhhhhhhheeeeeeeeeee....eeeeeee..eee...eee....ee.........eeeeeeeeeehhhhh....eeeeeeee..................eeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qjh D   2 MKVIQTPRYLVKGQGQKAKMRCIPEKGHPVVFWYQQNKNNEFKFLINFQNQEVLQQIDMTEKRFSAECPSNSPCSLEIQSSEAGDSALYLCASSLNNANSDYTFGSGTRLLVIEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRA 246
                                    11        21        31        41        51        61        71        81        91       101       111   ||  124       134       144       154       164       174       184       194       204       214       224       234       244  
                                                                                                                                           115|                                                                                                                               
                                                                                                                                            119
   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  (2, 8)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3QJH)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3QJH)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3QJH)

 Visualization

(-) Interactive Views

Asymmetric 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 3qjh)
 
  Sites
(no "Sites" information available for 3qjh)
 
  Cis Peptide Bonds
    Ser A:6 - Pro A:7   [ RasMol ]  
    Ser C:6 - Pro C:7   [ RasMol ]  
    Thr B:7 - Pro B:8   [ RasMol ]  
    Thr D:7 - Pro D:8   [ RasMol ]  
    Tyr B:154 - Pro B:155   [ RasMol ]  
    Tyr D:154 - Pro D:155   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 PNG format | Biol. Unit 2 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
  3qjh
    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 3QJH)

(-) Related Entries Specified in the PDB File

3qib 3qiw 3qjf