triangle PDBeMotif: 1sje  
  coner Sequences coner   coner 3D motifs coner   coner Ligand environment coner   coner Ligand bonds coner
   
coner
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coner
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Classification immune system    | release date: Wed, Mar 3, 2004
Title hla-dr1 complexed with a 16 residue hiv capsid peptide bound in a hairpin conformation
Authors B.D.WALKER, I.STRUG, L.J.STERN, P.J.NORRIS, Z.ZAVALA-RUIZ
Method X-RAY DIFFRACTION (resolution: 2.45Å)
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:
EEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALANIAVDKANLEIMTKRSNYTPI
TNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYD
CRVEHWGLDEPLLKHWEFDA
Chain B sequence:
GDTRPRFLWQLKFECHFFNGTERVRLLERCIYNQEESVRFDSDVGEYRAVTELGRPDAEYWNSQKDLLEQRRAAVDTYCR
HNYGVGESFTVQRRVEPKVTVYPSKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNGDWTFQTLVM
LETVPRSGEVYTCQVEHPSVTSPLTVEWRA
Chain C sequence:
PEVIPMFSALSEGATP
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: GENE3D: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...hhhhhh...hhhhhhhhhhhhhhhhhhhhhh..........eeeeee.........eeeeeeeeee.....eeeeee..eee....ee...ee.....eeeeeeeee......eeeeeee.......eeeeee...
sequence :  ..EEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEFDA
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  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 ..                                                                   *****                                                                                                            

chain B : HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DRB1-1BETA CHAIN;
member of: GENE3D: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  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 : GAG POLYPROTEIN
member of: GENE3D:searchG3DSA_1.10.375.10PFAM:searchPF00607SUPERFAMILY:searchSSF47943UniProt:searchP12495
sec str:  .................
sequence :  ..PEVIPMFSALSEGAT
seq num:  ..34        44   
search RasMol script viewer Motif-ligand binding stats  nest ..            ***

chain D : ENTEROTOXIN TYPE C-3
member of: GENE3D: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...hhhhhhhhh...eeeeee.........eeee...........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  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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