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 :  J809.B5 Y31A TCR BOUND TO IAB3K
 
Authors :  B. D. Stadinski, E. S. Huseby, P. Trenh, L. J. Stern
Date :  11 Mar 14  (Deposition) - 28 May 14  (Release) - 04 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.85
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Tcr Mhcii, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. D. Stadinski, P. Trenh, B. Duke, P. G. Huseby, G. Li, L. J. Stern, E. S. Huseby
Effect Of Cdr3 Sequences And Distal V Gene Residues In Regulating Tcr-Mhc Contacts And Ligand Specificity.
J Immunol. V. 192 6071 2014
PubMed-ID: 24813203  |  Reference-DOI: 10.4049/JIMMUNOL.1303209

(-) Compounds

Molecule 1 - H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, A-B ALPHA CHAIN
    ChainsC
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System CommonFALL ARMYWORM
    Expression System Taxid7108
    FragmentRESIDUES 27-205
    GeneH2-AA
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymIAALPHA
 
Molecule 2 - 3K PEPTIDE,H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, A BETA CHAIN
    ChainsD
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System CommonFALL ARMYWORM
    Expression System Taxid7108
    FragmentRESIDUES 30-218
    GeneH2-AB1, H2-IABETA
    Organism CommonHOUSE MOUSE
    Organism ScientificSYNTHETIC CONSTRUCT, MUS MUSCULUS
    Organism Taxid32630, 10090
 
Molecule 3 - J809.B5 TCR Y31A ALPHA CHAIN (VA2.8)
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    MutationYES
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
 
Molecule 4 - J809.B5 TCR BETA CHAIN (VB8.2)
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4P46)

(-) Sites  (0, 0)

(no "Site" information available for 4P46)

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1A:22 -A:90
2A:134 -A:184
3A:159 -B:167
4B:21 -B:89
5B:141 -B:206
6C:107 -C:163
7D:15 -D:79
8D:118 -D:174

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Ser C:15 -Pro C:16
2Phe C:113 -Pro C:114
3Tyr D:124 -Pro D:125
4Ser A:6 -Pro A:7
5Ser B:5 -Pro B:6
6Tyr B:147 -Pro B:148

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4P46)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4P46)

(-) Exons   (0, 0)

(no "Exon" information available for 4P46)

(-) 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:199
                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eeeee....eeeeeee......eeeeeee......eeeeeee....eeee..eeeeee....eeeeee...hhhhheeeeeee.......ee...eeeeee........eeeeeee......eeeeee...............eee...eeee......eeeeeeeee........................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p46 A   2 QVRQSPQSLTVWEGETAILNCSYENSAFDAFPWYQQFPGEGPALLIAIRSVSDKKEDGRFTIFFNKREKKLSLHITDSQPGDSATYFCAASKGADRLTFGKGTQLIIQPYIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPS 201
                                    11        21        31        41        51  ||    62        72        82        92       102       112       122       132       142       152       162       172       182       192         
                                                                               54|                                                                                                                                                 
                                                                                56                                                                                                                                                 

Chain B from PDB  Type:PROTEIN  Length:238
                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eeeee....eeeeeee.....eeeeeeee...eeeeeeee......ee......eeee......eeeee...hhhhheeeeeeee.......ee...eeeeee.........eeeeee.hhhhhhhhheeeeeeeeeee....eeeeeee..eee...eee....ee.........eeeeeeeeeehhhhh....eeeeeeee..................eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p46 B   1 AVTQSPRNKVAVTGGKVTLSCNQTNNHNNMYWYRQDTGHGLRLIHYSYGAGSTEKGDIPDGYKASRPSQENFSLILELATPSQTSVYFCASGDFWGDTLYFGAGTRLSVLEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGR 238
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230        

Chain C from PDB  Type:PROTEIN  Length:179
                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeeee...eeeeeeee..eeeeeee....eeee.hhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..........eeeeee.........eeeeeeeeee.....eeeeee..eee....ee...ee.....eeeeeeeee.......eeeeee.......eeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p46 C   0 IEADHVGTYGISVYQSPGDIGQYTFEFDGDELFYVDLDKKETVWMLPEFGQLASFDPQGGLQNIAVVKHNLGVLTKRSNSTPATNEAPQATVFPKSPVLLGQPNTLICFVDNIFPPVINITWLRNSKSVADGVYETSFFVNRDYSFHKLSYLTFIPSDDDIYDCKVEHWGLEEPVLKHW 178
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169         

Chain D from PDB  Type:PROTEIN  Length:200
                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeeeeeeeee....eeeeeeeeee..eeeeeee......ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh....eeeeee.........eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeee......eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p46 D -25 FEAQKAKANKAVDHFVYQFMGECYFTNGTQRIRYVTRYIYNREEYVRYDSDVGEHRAVTELGRPDAEYWNSQPEILERTRAELDTVCRHNYEGPETHTSLRRLEQPNVVISLSRTEALNHHNTLVCSVTDFYPAKIKVRWFRNGQEETVGVSSTQLIRNGDWTFQVLVMLEMTPRRGEVYTCHVEHPSLKSPITVEWRAQ 192
                                   -16  ||    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192
                                      -13|                                                                                                                                                                                          
                                         6                                                                                                                                                                                          

   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 4P46)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4P46)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4P46)

(-) Gene Ontology  (41, 61)

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
(no "Ligands, Modified Residues, Ions" information available for 4p46)
 
  Sites
(no "Sites" information available for 4p46)
 
  Cis Peptide Bonds
    Phe C:113 - Pro C:114   [ RasMol ]  
    Ser A:6 - Pro A:7   [ RasMol ]  
    Ser B:5 - Pro B:6   [ RasMol ]  
    Ser C:15 - Pro C:16   [ RasMol ]  
    Tyr B:147 - Pro B:148   [ RasMol ]  
    Tyr D:124 - Pro D:125   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4p46
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  HA2B_MOUSE | P14434
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
  HB2A_MOUSE | P14483
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
  TRBC1_HUMAN | P01850
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  HA2B_MOUSE | P14434
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  HB2A_MOUSE | P14483
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  TRBC1_HUMAN | P01850
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        HA2B_MOUSE | P144341lnu 1muj 3c5z 3c60 3c6l 3rdt 4p23 4p5t
        HB2A_MOUSE | P144831lnu 1muj 3c5z 3c60 3c6l 3rdt 4p23 4p5t
        TRBC1_HUMAN | P018501ao7 1fyt 1j8h 1kgc 1ktk 1mi5 1oga 1ymm 1zgl 2ak4 2axh 2bnq 2bnr 2bnu 2cde 2cdf 2cdg 2esv 2f53 2f54 2gj6 2ial 2iam 2ian 2nts 2nw2 2nx5 2p5e 2p5w 2po6 2pye 2pyf 2vlj 2vlk 2vlm 2vlr 2xn9 2xna 3arb 3ard 3are 3arf 3arg 3d39 3d3v 3dx9 3dxa 3ffc 3he6 3hg1 3kpr 3kps 3o4l 3tn0 4g8e 4g8f 4gg6 4gg8 4iiq 4jfd 4jfe 4jff 4jfh 4jrx 4jry 4l4t 4l4v 4l9l 4lcc 4lcw 4mji 4mnq 4nqc 4nqd 4nqe 4ozf 4ozg 4ozh 4ozi 4prh 4pri 4prp 4x6b 4x6c 4x6d 4zdh

(-) Related Entries Specified in the PDB File

4p23 4P23 CONTAINS THE WILDTYPE T CELL RECEPTOR COMPLEXED WITH THE SAME PMHC LIGAND - NATIVE STRUCTURE