triangle PDBeMotif: 1t5x  
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Classification immune system    | release date: Wed, May 5, 2004
Title hla-dr1 in complex with a synthetic peptide (aaysdqatplllspr) and the superantigen sec3-3b2
Authors I.STRUG, J.GORSKI, L.J.STERN, M.W.ANDERSON, Z.ZAVALA-RUIZ
Method X-RAY DIFFRACTION (resolution: 2.50Å)
PDBe Citation   
Ligand bond colours:   *  covalent   *  ionic   *  hydrogen   *  electrostatic   *  van-der-waals   *  plane-atom   *  plane-plane   *  undefined  - Click here to show 5Å bonds
Chain A sequence:
KEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALANIAVDKANLEIMTKRSNYTP
ITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVY
DCRVEHWGLDEPLLKHWEFDA
Chain B sequence:
GDTRPRFLWQLKFECHFFNGTERVRLLERCIYNQEESVRFDSDVGEYRAVTELGRPDAEYWNSQKDLLEQRRAAVDTYCR
HNYGVGESFTVQRRVEPKVTVYPSKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNGDWTFQTLVM
LETVPRSGEVYTCQVEHPSVTSPLTVEWRA
Chain C sequence:
AAYSDQATPLLLSPR
Chain D sequence:
ESQPDPMPDDLHKSSEFTGTMGNMKYLYDDHYVSATKVKSVDSFFKWDLIYNISDKKLKNYDKVKTELLNEDLAKKYKDE
VVDVYGSNYYVNCYFSSKDNVGKVTGGKTCMYGGITKHEGNHFDNGNLQNVLVRVYENKRNTISFEVQTDKKSVTAQELD
IKARNFLINKKNLYEFNSSPYETGYIKFIENNGNTFWYDMMPAPGDKFDQSKYLMMYNDNKTVDSKSVKIEVHLTTKNG
Residue colours:  hydrophilic   hydrophobic   intermediate 
Assembly 1     View the assembly/model: ( JMolViewer Download PDB file RasMol script viewer AstexViewer™@MSD-EBI )
Motif search   chain:    Sequence numbers: 
   Using:   φ/ψ    residues code    secondary structures   
 coordinates of:  Cαs Side-chain
 
      View the fragment: rasmol script JMol viewer
chain A : HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DRALPHA CHAIN;
member of: CATH:search2.60.40.10/search3.10.320.10GENE3D:searchG3DSA_2.60.40.10/searchG3DSA_3.10.320.10PANTHER:searchPTHR19944/searchPTHR19944_SF27PFAM:searchPF00993/searchPF07654PROSITE PATTERNS:searchPS00290, PROSITE PROFILES:searchPS50835, SMART:searchSM00407/searchSM00920SUPERFAMILY:searchSSF48726/searchSSF54452UniProt:searchP01903
sec str:  ...eeeeeeeeeee...eeeeeeee..eeeeeee....eeee.hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh..........eeeeee.........eeeeeeeeee.....eeeeee..eee....ee...ee.....eeeeeeeee......eeeeeee.......eeeeee...
sequence :  ..EHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEFDA
seq num:  ..4         14        24        34        44        54        64        74        84        94        104       114       124       134       144       154       164       174      
search RasMol script viewer Motif-ligand binding stats  ASN_GLYCOSYLATION ..          |  | |      |  |     | || ||     ||||||     |    |      |   ||||||               |  |  |            | | ^***      |||||   |   | |||           |  | | |   |  |            
search RasMol script viewer Motif-ligand binding stats  CAMP_PHOSPHO_SITE ..          |  | |      |  |     | |**^*     ||||||     |    |      |   ||||||               |  |  |            | |           |||||   |   | |||           |  | | |   |  |            
search RasMol script viewer Motif-ligand binding stats  PKC_PHOSPHO_SITE ..          |  | |      |  |     | || |      ||||||     |    |      |   ^**|||               |  |  |            | |           |||||   |   | |||           |  | | |   |  |            
search RasMol script viewer Motif-ligand binding stats  CK2_PHOSPHO_SITE ..          |  | |      |  |     | || |      ||||||     |    |      |   || |||               ^***  |            | |           |||||   |   | |||           ^*** | |   |  |            
search RasMol script viewer Motif-ligand binding stats  MYRISTYL ..          |  | |      |  |     | || |      ||||||     ^*****      |   || |||                  |  |            | |           |||^*****   | |||           |  | | |   |  |            
search RasMol script viewer Motif-ligand binding stats  IG_MHC ..          |  | |      |  |     | || |      ||||||                 |   || |||                  |  |            | |           ||| |       | |||           |  | **^****  |            
search RasMol script viewer Motif-ligand binding stats  alphabetamotif ..          |  | |      |  |     | || |      |*****                 |   || |||                  |  |            | |           ||| |       | |||           |  |       |  |            
search RasMol script viewer Motif-ligand binding stats  asxturn ..          |  | |      |  |     ***| |      ||||||                 |   || |||                  |  |            | |           ||| |       | ***           |  |       |  |            
search RasMol script viewer Motif-ligand binding stats  betabulgeloop ..          ******      |  |        | |      ||||||                 |   || |||                  |  |            | |           ||| |       | |||           |  |       |  |            
search RasMol script viewer Motif-ligand binding stats  betaturn ..             | |      ****        | |      *****|                 |   |****|                  ****            | |           ||| |       ****|           |  |       ****            
search RasMol script viewer Motif-ligand binding stats  gammaturn ..             | |                  | |        |  |                 |   |  | |                  |  |            ***           ||| |         | |           |  |       |  |            
search RasMol script viewer Motif-ligand binding stats  nest ..             ***                  ***        |  |                 |   |  ***                  |  |                          ||| |         ***           |  |       |  |            
search RasMol script viewer Motif-ligand binding stats  niche ..                                             ****                 |   |    |                  ****                          *****                       ****       ****            
search RasMol script viewer Motif-ligand binding stats  schellmannloop ..                                                                  |   ******                                                                                                       
search RasMol script viewer Motif-ligand binding stats  ststaple ..                                                                  *****                                                                                                            

chain B : HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DRB1-1BETA CHAIN;
member of: CATH:search2.60.40.10/search3.10.320.10GENE3D:searchG3DSA_2.60.40.10/searchG3DSA_3.10.320.10PANTHER:searchPTHR19944/searchPTHR19944_SF42PFAM:searchPF00969/searchPF07654PRODOM:searchPD000328PROSITE PATTERNS:searchPS00290, PROSITE PROFILES:searchPS50835, SMART:searchSM00407/searchSM00921SUPERFAMILY:searchSSF48726/searchSSF54452UniProt:searchP04229
sec str:  ........eeeeeeeeeeee....eeeeeeeee....eeeeee.....eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeee.........eeeeeeeeee.....eeeeee..ee....eee...ee.....eeeeeeeee......eeeeeee.......eeeeee.
sequence :  ..GDTRPRFLWQLKFECHFFNGTERVRLLERCIYNQEESVRFDSDVGEYRAVTELGRPDAEYWNSQKDLLEQRRAAVDTYCRHNYGVGESFTVQRRVEPKVTVYPSKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSVTSPLTVEWRA
seq num:  ..1         11        21        31        41        51        61        71        81        91        101       111       121       131       141       151       161       171       181       
search RasMol script viewer Motif-ligand binding stats  ASN_GLYCOSYLATION .. | |              ^***| |      |    | | | || ||   |  ||       | ||    | || ||      | |  ||  |                | |      |  | | |            | || | |   |||||           |  | | |   |  |          
search RasMol script viewer Motif-ligand binding stats  PKC_PHOSPHO_SITE .. | |                ^** |      |    ^** | || ||   |  ||       ^**|    | || ||      | |  ||  |                | |      |  | | |            | || | |   |||||           |  | | |   |  |          
search RasMol script viewer Motif-ligand binding stats  CK2_PHOSPHO_SITE .. | |                    |      |      | | || ||   |  ||       ^***    | || ||      | |  ||  |                | |      |  | | |            | || | |   |||||           |  | | |   |  |          
search RasMol script viewer Motif-ligand binding stats  TYR_PHOSPHO_SITE .. | |                    *******^      ********^   |  ||               | || ||      | |  ||  |                | |      |  | | |            | || | |   |||||           |  | | |   |  |          
search RasMol script viewer Motif-ligand binding stats  MYRISTYL .. | |                                    | || |    |  ||               | || ||      ^*****|  |                | |      |  | | |            | ^*****   |||||           |  | | |   |  |          
search RasMol script viewer Motif-ligand binding stats  IG_MHC .. | |                                    | || |    |  ||               | || ||        |   |  |                | |      |  | | |            |  | | |   |||||           |  | **^****  |          
search RasMol script viewer Motif-ligand binding stats  alphabetamotif .. | |                                    | || |    *****               | *****        |   |  |                | |      |  | | |            |  | | |   |||||           |  |       |  |          
search RasMol script viewer Motif-ligand binding stats  asxturn .. | |                                    ***| |    |  |                | || |         |   |  |                | |      |  | | |            |  | | |   |||||           |  |       |  |          
search RasMol script viewer Motif-ligand binding stats  betaturn .. | |                                       | |    ****                ******         |   |  |                | |      |  | | |            |  | | |   |||||           ****       |  |          
search RasMol script viewer Motif-ligand binding stats  gammaturn .. | |                                       | |                                       |   |  |                ***      |  | | |            |  | | |   |||||           |  |       |  |          
search RasMol script viewer Motif-ligand binding stats  nest .. | |                                       ***                                       |   |  |                         |  | | |            |  | | |   *****           |  |       |  |          
search RasMol script viewer Motif-ligand binding stats  niche .. ***                                                                                 |   ****                         **** ***            **** | |                   ****       ****          
search RasMol script viewer Motif-ligand binding stats  ststaple ..                                                                                     *****                                                     | |                                            
search RasMol script viewer Motif-ligand binding stats  stturn ..                                                                                                                                               ***                                            

chain C : 15-MER PEPTIDE FRAGMENT OF REGULATORY PROTEINMIG1;
member of: UniProt:searchP27705
sec str:  ...............
sequence :  ..AAYSDQATPLLLS
seq num:  ..0         10 
search RasMol script viewer Motif-ligand binding stats  PKC_PHOSPHO_SITE ..            ^

chain D : ENTEROTOXIN TYPE C-3
member of: CATH:search2.40.50.110/search3.10.20.120GENE3D:searchG3DSA_2.40.50.110/searchG3DSA_3.10.20.120PFAM:searchPF01123/searchPF02876PRINTS:searchBACTRLTOXIN/searchSAGSUPRFAMLYPROSITE PATTERNS:searchPS00277/searchPS00278, SUPERFAMILY:searchSSF50203/searchSSF54334UniProt:searchP0A0L5
sec str:  ........hhhhh.hhhhh...hhhhhh......eeeeee.........eeeee..........eeeee..hhhhhhhhhh..eeeee..............eeeee..eee...........eeeeeeeee..eeeeeeeeee...eeehhhhhhhhhhhhhhhhh..........eeeeeee.....eeeee.........hhhhhhhhhhhh.eee....eeeeeee....
sequence :  ..ESQPDPMPDDLHKSSEFTGTMGNMKYLYDDHYVSATKVKSVDSFFKWDLIYNISDKKLKNYDKVKTELLNEDLAKKYKDEVVDVYGSNYYVNCYFS..GGKTCMYGGITKHEGNHFDNGNLQNVLVRVYENKRNTISFEVQTDKKSVTAQELDIKARNFLINKKNLYEFNSSPYETGYIKFIENNGNTFWYDMMPAPGDKFDQSKYLMMYNDNKTVDSKSVKIEVHLTTKNG
seq num:  ..1         11        21        31        41        51        61        71        81        91    ..106       116       126       136       146       156       166       176       186       196       206       216       226       236 
search RasMol script viewer Motif-ligand binding stats  ASN_GLYCOSYLATION .. |  | || || || || ||| ||||  |  |            |  |   ^***| ||||               |  |        ||| |  |..|  | ||   || ||||   |    |       | ||      | | | |  ||           ||||    | |||      | |||    | |       |   |     |^*** | |||     | |  
search RasMol script viewer Motif-ligand binding stats  CAMP_PHOSPHO_SITE .. |  | || || || || ||| ||||  |  |            |  |     | | ||||               |  |        ||| |  |..|  | ||   || ||||   |    |       **^*      | | | |  ||           ||||    | |||      | |||    | |       |   |     | |   | |||     | |  
search RasMol script viewer Motif-ligand binding stats  PKC_PHOSPHO_SITE .. |  | || || || || ||| ||||  |  |            |  |     ^** ||||               |  |        ||| |  ^..|  | ||   || ||||   |    |                 ^** | |  ||           ||||    | |||      | |||    | |       |   |     | |   | ^**     ^**  
search RasMol script viewer Motif-ligand binding stats  CK2_PHOSPHO_SITE .. ^*** || || || || ||| ||||  |  |            |  |         ||||               |  |        ||| |  ^..|  | ||   ^***|||   |    |                 | | | ^***|           ||||    ^***|      | |||    | |       |   |     | |   |  |           
search RasMol script viewer Motif-ligand binding stats  TYR_PHOSPHO_SITE ..      || || || || ||| ||*******^            |  |         ||||               |  |        ||| |   ..|  | ||    | ||||   |    |                 | | | |   |           ||||    | |||      | |||    | |       |   |     | |   |  |           
search RasMol script viewer Motif-ligand binding stats  MYRISTYL ..      || || || || ^*****||  |               |  |         ||||               |  |        ||| |   ..^*****|    | ||||   ^*****                 | | | |   |           ||||    | |||      | |||    | |       |   |     | |   |  |           
search RasMol script viewer Motif-ligand binding stats  ATP_GTP_A ..      || || || ||  || ||||  |               |  |         ||||               |  |        ||| |   ..****  |    | ||||                          | | | |   |           ||||    | |||      | |||    | |       |   |     | |   |  |           
search RasMol script viewer Motif-ligand binding stats  STAPH_STREP_TOXIN_1 ..      || || || ||  || ||||  |               |  |         ||||               |  |        ||| |   ..      **********|                          | | | |   |           ||||    | |||      | |||    | |       |   |     | |   |  |           
search RasMol script viewer Motif-ligand binding stats  STAPH_STREP_TOXIN_2 ..      || || || ||  || ||||  |               |  |         ||||               |  |        ||| |   ..           | || |                          | ************************    | |||      | |||    | |       |   |     | |   |  |           
search RasMol script viewer Motif-ligand binding stats  alphabetamotif ..      || || || ||  |*****|  |               |  |         ||||               |  |        ||| |   ..           | || |                          | | | |   |           ||||    | |||      | |||    | |       |   |     | |   |  |           
search RasMol script viewer Motif-ligand binding stats  asxmotif ..      || || || ||  || || |  |               |  |         ||||               |  |        ||| |   ..           | || |                          | | | |   |           ||||    | |||      | |||    | |       *****     | |   |  |           
search RasMol script viewer Motif-ligand binding stats  asxturn ..      || || || ||  || || |  |               |  |         ||||               |  |        ||| |   ..           | || |                          | | | |   |           ||||    | |||      | ***    ***                 | |   |  |           
search RasMol script viewer Motif-ligand binding stats  betabulge ..      || || || ||  || || |  |               |  |         ||||               |  |        ||| |   ..           | || |                          | | | |   |           ||||    | |**      | |||    | |                 | |   |  |           
search RasMol script viewer Motif-ligand binding stats  betabulgeloop ..      || || || ||  || || |  |               |  |         ||||               |  |        ||| |   ..           | || |                          | | | |   |           ||||    | |        *****    | |                 | |   |  |           
search RasMol script viewer Motif-ligand binding stats  betaturn ..      ****| *****  ***** |  |               |  |         ||||               ****        ||| |   ..           | || |                          | | | |   |           ||||    | |        ****|    | |                 | |   |  |           
search RasMol script viewer Motif-ligand binding stats  nest ..       |  |  |  |        |  |               |  |         ****               |  |        ||| |   ..           | |***                          | | | |   |           ****    | |          ***    | |                 ***   |  |           
search RasMol script viewer Motif-ligand binding stats  niche ..       ****  ****        ****               ****                            ****        *****   ..           ***                             | *** |   |                   ***                 ***                       ****           
search RasMol script viewer Motif-ligand binding stats  stmotif ..                                                                                                ..                                           | |   *****                   | |                                                          
search RasMol script viewer Motif-ligand binding stats  stturn ..                                                                                                ..                                           ***                           ***                                                          

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