triangle PDBeMotif: 1pyw  
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Classification immune system/protein binding/toxin    | release date: Wed, Jul 9, 2003
Title human class ii mhc protein hla-dr1 bound to a designed pepti to influenza virus hemagglutinin, fvkqna(maa)al, in complex staphylococcal enterotoxin c3 variant 3b2 (sec3-3b2)
Authors D.B.DEOLIVEIRA, E.J.SUNDBERG, I.C.CHAN, J.D.STONE, J.SVENDSEN, L.J.STERN, R.A.MARIUZZA, Z.ZAVALA-RUIZ
Method X-RAY DIFFRACTION (resolution: 2.10Å)
PDBe Citation   
Small molecules:    search ACE ACE binding statistics ACE
Modified residues:  search MAA MAA binding statistics MAA
Ligand bond colours:   *  covalent   *  ionic   *  hydrogen   *  electrostatic   *  van-der-waals   *  plane-atom   *  plane-plane   *  undefined  - Click here to show 5Å bonds
Chain A sequence:
IKEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALANIAVDKANLEIMTKRSNYT
PITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDV
YDCRVEHWGLDEPLLKHWEFDA
Chain B sequence:
GDTRPRFLWQLKFECHFFNGTERVRLLERCIYNQEESVRFDSDVGEYRAVTELGRPDAEYWNSQKDLLEQRRAAVDTYCR
HNYGVGESFTVQRRVEPKVTVYPSKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNGDWTFQTLVM
LETVPRSGEVYTCQVEHPSVTSPLTVEWRA
Chain C sequence:
FVKQNAAAL
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, DR ALPHA
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 0C  ..                                                 *                                                                                                                                 
sec str:  ...eeeeeeeeeee...eeeeeeee..eeeeeee....eeee...hhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..........eeeeee.........eeeeeeeeee.....eeeeee..ee.....ee...ee.....eeeeeeeee.......eeeeee.......eeeee....
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, DR-1 BET
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
JMol viewer RasMol script viewer  ACE 0C  ..                                                                                *                                                                                                             
sec str:  ........eeeeeeeeeeee....eeeeeeeee....eeeeee.....eee.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.......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  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 : 9-RESIDUE INFLUENZA VIRUS HEMAGGLUTININ RELATED PFVKQNA(MAA)AL;
member of: GB:search3212739
JMol viewer RasMol script viewer  ACE 0C  ..**       
sec str:  ...........
sequence :  ..FVKQNAAAL
seq num:  ..1        

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:searchP0A0L3
sec str:  ........hhhhh.hhhhh...hhhhhhhhh...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  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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