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Classification viral protein/immune system    | release date: Sun, Nov 25, 2001
Title structure of the epstein-barr virus gp42 protein bound to the mhc class ii receptor hla-dr1
Authors K.M.HAAN, M.M.MULLEN, R.LONGNECKER, T.S.JARDETZKY
Method X-RAY DIFFRACTION (resolution: 2.65Å)
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:
TRPRFLWQLKFECHFFNGTERVRLLERCIYNQEESVRFDSDVGEYRAVTELGRPDAEYWNSQKDLLEQRRAAVDTYCRHN
YGVGESFTVQRRVEPKVTVYPSKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNGDWTFQTLVMLE
TVPRSGEVYTCQVEHPSVTSPLTVEWRA
Chain D sequence:
PKYVKQNTLKLAT
Chain C sequence:
HTFQVPQNYTKANCTYCNTREYTFSYKGCCFYFTKKKHTWNGCFQACAEKYPCTYFYGPTPDILPVVTRNLNAIESLWVG
VYRVGEGNWTSLDGGTFKVYQIFGSHCTYVSKFSTVPVSHHECSFLKPCLCVSQRS
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 : MHC CLASS II RECEPTOR HLA-DR1
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.hhhhhh....hhhhhhhhhhhhhhhhhhhhhhh..........eeeeee.........eeeeeeeeee.....eeeeee..ee.....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  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 : MHC CLASS II RECEPTOR HLA-DR1
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.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.........eeeeee.........eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeee......eeeeeee.......eeeeee.
sequence :  ..TRPRFLWQLKFECHFFNGTERVRLLERCIYNQEESVRFDSDVGEYRAVTELGRPDAEYWNSQKDLLEQRRAAVDTYCRHNYGVGESFTVQRRVEPKVTVYPSKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSVTSPLTVEWRA
seq num:  ..3         13        23        33        43        53        63        73        83        93        103       113       123       133       143       153       163       173       183     
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  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 D : HEMAGGLUTININ HA PEPTIDE
sec str:  ...............
sequence :  ..PKYVKQNTLKLAT
seq num:  ..306          
search RasMol script viewer Motif-ligand binding stats  PKC_PHOSPHO_SITE ..       ^**   

chain C : GP42 PROTEIN
member of: CATH:search3.10.100.10GENE3D:searchG3DSA_3.10.100.10PFAM:searchPF00059SMART:searchSM00034SUPERFAMILY:searchSSF56436UniProt:searchP03205
sec str:  .........................eee..eeeee.......hhhhhhhhhhh...ee......hhhhhhhh......ee..eee.....eee................eee.......ee..........eeeee..
sequence :  ..HTFQVPQNYTKANCTYCNTREYTFSYKGCCFYFTKKKHTWNGCFQACAEKYPCTYFYGPTPDILPVVTRNLNAIESLWVGVYRVGEGNWTSLDGGTFKVYQIFGSHCTYVSKFSTVPVSHHECSFLKPCLCVSQRS
seq num:  ..86        96        106       116       126       136       146       156       166       176       186       196       206       216   
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  betaturn ..                  |  |           | |  |   |    |  |  |     ****    |  ||  |               ****         |  |   | ||       |  |           
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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