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Classification immune system    | release date: Thu, Oct 12, 2006
Title crystal structure of the mhc class ii molecule hla-dr1 in complex with the fluorogenic peptide, acpkxvkqntlklat (x=3- [5-(dimethylamino)-1,3-dioxo-1,3-dihydro-2h-isoindol-2-yl]- l-alanine) and the superantigen, sec3 variant 3b2
Authors L.J.STERN, T.T.NGUYEN
Method X-RAY DIFFRACTION (resolution: 2.30Å)
PDBe Citation   
Small molecules:    search ACE ACE binding statistics ACE
Modified residues:  search 4DP 4DP binding statistics 4DP
Ligand bond colours:   *  covalent   *  ionic   *  hydrogen   *  electrostatic   *  van-der-waals   *  plane-atom   *  plane-plane   *  undefined  - Click here to show 5Å bonds
Chain A sequence:
MIKEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALANIAVDKANLEIMTKRSNY
TPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTED
VYDCRVEHWGLDEPLLKHWEFDA
Chain B sequence:
GDTRPRFLWQLKFECHFFNGTERVRLLERCIYNQEESVRFDSDVGEYRAVTELGRPDAEYWNSQKDLLEQRRAAVDTYCR
HNYGVGESFTVQRRVEPKVTVYPSKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNGDWTFQTLVM
LETVPRSGEVYTCQVEHPSVTSPLTVEWRA
Chain C sequence:
PKWVKQNTLKLAT
Chain D sequence:
MESQPDPMPDDLHKSSEFTGTMGNMKYLYDDHYVSATKVKSVDSFFKWDLIYNISDKKLKNYDKVKTELLNEDLAKKYKD
EVVDVYGSNYYVNCYFSSKDNVGKVTGGKTCMYGGITKHEGNHFDNGNLQNVLVRVYENKRNTISFEVQTDKKSVTAQEL
DIKARNFLINKKNLYEFNSSPYETGYIKFIENNGNTFWYDMMPAPGDKFDQSKYLMMYNDNKTVDSKSVKIEVHLTTKNG
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
JMol viewer RasMol script viewer  ACE 305C  ..                                                                                                                                                                                   
sec str:  ....eeeeeeeeeee...eeeeeeee..eeeeeee....eeee...hhhhhh...hhhhhhhhhhhhhhhhhhhhhh..........eeeeee.........eeeeeeeeee.....eeeeee..eee....ee...ee.....eeeeeeeee......eeeeeee.......eeeeee..
sequence :  ..EEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEFD
seq num:  ..3         13        23        33        43        53        63        73        83        93        103       113       123       133       143       153       163       173      
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  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....eeeeeeeeee..eeeeeee.....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  asxmotif .. | |                                    *****|    |  |      |  |                     |   |  |                         |  | | |            |  | | |   |||||           |  |       |  |          
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  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 : HA RELATED FLUOROGENIC PEPTIDE, ACPKXVKQNTLKLAT(X=3-[5-(DIMETHYLAMINO)-1,3-DIOXO-1,3-DIHYDRO-2H-ISOINDOL-2-YL]-L-ALANINE);
member of: GENE3D:searchG3DSA_3.90.20.10PFAM:searchPF00509PRINTS:searchHEMAGGLUTN1/searchHEMAGGLUTN12SUPERFAMILY:searchSSF49818UniProt:searchA8CDU0
JMol viewer RasMol script viewer  ACE 305C  ..**           
sec str:  ...............
sequence :  ..PKWVKQNTLKLAT
seq num:  ..306          
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 :  ..ESQPDPMPDDLHKSSEFTGTMGNMKYLYDDHYVSATKVKSVDSFFKWDLIYNISDKKLKNYDKVKTELLNEDLAKKYKDEVVDVYGSNYYVNCYFSSK..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  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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