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 :  STRUCTURE OF THE DP10.7 TCR
 
Authors :  A. M. Luoma, E. J. Adams
Date :  10 Sep 13  (Deposition) - 18 Dec 13  (Release) - 14 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Immunoglobulin, Histocompatibility Antigens, T Cell Receptor, Immunological, Lymphocytes, T Cell Recognition, Activation, Gamma Delta T Cell, Human, Intraepithelial Lymphocytes, Cd1D, Glycolipids, Non-Classical Mhc, Glycoproteins, Cell-Surface Receptors, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. M. Luoma, C. D. Castro, T. Mayassi, L. A. Bembinster, L. Bai, D. Picard, B. Anderson, L. Scharf, J. E. Kung, L. V. Sibener, P. B. Savage, B. Jabri, A. Bendelac, E. J. Adams
Crystal Structure Of V Delta 1 T Cell Receptor In Complex With Cd1D-Sulfatide Shows Mhc-Like Recognition Of A Self-Lipid By Human Gamma Delta T Cells.
Immunity V. 39 1032 2013
PubMed-ID: 24239091  |  Reference-DOI: 10.1016/J.IMMUNI.2013.11.001

(-) Compounds

Molecule 1 - T-CELL RECEPTOR GAMMA CHAIN V REGION PT-GAMMA-1/2, HUMAN NKT TCR BETA CHAIN
    Chains: A, C
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Taxid: 7111
    Fragment: DP10.7 TCR GAMMA VARIABLE DOMAIN FUSED WITH HUMAN TCR BETA CONSTANT DOMAIN
    Gene: TRGV3, TCRB, B2M, HDCMA22P, B2M, HDCMA22P
    Mutation: YES
    Organism Common: HUMAN, HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - HUMAN NKT TCR ALPHA CHAIN
    Chains: B, D
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Taxid: 7111
    Fragment: DP10.7 TCR DELTA VARIABLE DOMAIN FUSED WITH HUMAN TCR ALPHA CONSTANT DOMAIN
    Gene: TRA@
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 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 4MNH)

(-) Sites  (0, 0)

(no "Site" information available for 4MNH)

(-) SS Bonds  (10, 10)

Asymmetric Unit
No.Residues
1A:23 -A:95
2A:147 -A:212
3A:173 -B:167
4B:23 -B:91
5B:142 -B:192
6C:23 -C:95
7C:147 -C:212
8C:173 -D:167
9D:23 -D:91
10D:142 -D:192

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Tyr A:153 -Pro A:154
2Gly C:72 -Ser C:73
3Tyr C:153 -Pro C:154
4Lys D:3 -Val D:4
5Trp D:99 -Gly D:100
6Gly D:100 -Phe D:101

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4MNH)

(-) 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:231
                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee....eeee......eeeeeee......eeeeeee.....eee........eeee..eeee...hhhhheeeeeeee......eee...eeeeee.hhhhh...eeeee..hhhhhhhh.eeeeeeeeeee....eeeeeee..ee....eee....ee.........eeeeeeeeeehhhhh....eeeeeeee..................eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mnh A   8 TKSVIRQTGSSAEITCDLATGYIHWYLHQEGKAPQRLLYYDSYTSSVVLESGISPGKYDTYGLRMILRNLIENDSGVYYCATWDEKYYKKLFGSGTTLVVTEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD 246
                                    17        30        40        50        60        70 ||     85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245 
                                             26|                                        72|                                                                                                                                                                        
                                              30                                         78                                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:197
                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee....eee...........eeeeeee.....eeeeeeee......ee..eeeeee....eeeeee...hhhhheeeeeeee............eee...eeeeee........eeee........eeee..............ee...eeeee....eeeeeeeee................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mnh B   2 QKVTQAQSSVSMPVRKAVTLNCLYETSWWSYYIFWYKQLPSKEMIFLIRQGSDEQNAKSGRYSVNFKKAAKSVALTISALQLEDSAKYFCALGEPSYWGFPRTTRVIFGKGTRVTVEPNIQNPDPAVYQLRDSKSSVCLFTDFDSQTNVSQSKDVYITDKCVLDMRSMDFKSNSAVAWSNFACANAFNNSIPEDTFF 207
                                    11        21        31        41        51        61        71        81        91       101       111       121       131     ||144       154   ||  166       176       186|      199||     
                                                                                                                                                                 137|              158|                      186|       200|     
                                                                                                                                                                  141               161                       190        202     


Chain C from PDB  Type:PROTEIN  Length:236
                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee....eeeee......eeeeeee......eeeeeee.....eee........eeee...eeeee...hhhhheeeeeeee......eee...eeeeee.hhhhh...eeeee..hhhhhhhh.eeeeeeeeeee....eeeeeee..ee....eee....ee.........eeeeeeeeeehhhhh....eeeeeeee..................eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mnh C   6 GRTKSVIRQTGSSAEITCDLASTGYIHWYLHQEGKAPQRLLYYDSYTSSVVLESGISPGKYDTYGSNLRMILRNLIENDSGVYYCATWDEKYYKKLFGSGTTLVVTEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD 246
                                    15        25||      37        47        57        67     || 80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240      
                                               26|                                          73|                                                                                                                                                                         
                                                29                                           77                                                                                                                                                                         


Chain D from PDB  Type:PROTEIN  Length:199
                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee.....eee...........eeeeeee.....eeeeeeee......ee..eeeeee....eeeeee...hhhhheeeeeeee....hhhhh.eee...eeeee.....eeeeee.......eeeeee...............eee...eeee.....eeeeeeeee...................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mnh D   2 QKVTQAQSSVSMPVRKAVTLNCLYETSWWSYYIFWYKQLPSKEMIFLIRQGSDEQNAKSGRYSVNFKKAAKSVALTISALQLEDSAKYFCALGEPWGFPRTTRVIFGKGTRVTVENPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMSMDFKSNSAVAWSNKFACANAFNNSIIPEDTFFPS 209
                                    11        21        31        41        51        61        71        81        91    || 103       113    || 127       137       147       157       167   ||  178       190       200         
                                                                                                                         96|                118|                                             171|           187|                   
                                                                                                                          99                 123                                              173            190
   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 4MNH)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4MNH)

 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 4mnh)
 
  Sites
(no "Sites" information available for 4mnh)
 
  Cis Peptide Bonds
    Gly C:72 - Ser C:73   [ RasMol ]  
    Gly D:100 - Phe D:101   [ RasMol ]  
    Lys D:3 - Val D:4   [ RasMol ]  
    Trp D:99 - Gly D:100   [ RasMol ]  
    Tyr A:153 - Pro A:154   [ RasMol ]  
    Tyr C:153 - Pro C:154   [ 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
  4mnh
    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
  K7N5M3_HUMAN | K7N5M3
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
  K7N5M4_HUMAN | K7N5M4
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
  Q6PJ56_HUMAN | Q6PJ56
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
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
  K7N5M3_HUMAN | K7N5M3
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  K7N5M4_HUMAN | K7N5M4
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  Q6PJ56_HUMAN | Q6PJ56
    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
        K7N5M3_HUMAN | K7N5M3: 5e6i 5men
        K7N5M4_HUMAN | K7N5M4: 5brz 5bs0 5men
UniProtKB/TrEMBL
        K7N5M3_HUMAN | K7N5M3: 4en3 4mji 4ndm 4zak
        K7N5M4_HUMAN | K7N5M4: 4en3 4ndm
        Q6PJ56_HUMAN | Q6PJ56: 4lfh 4lhu 4mng 4ndm

(-) Related Entries Specified in the PDB File

4mng