triangle PDBeMotif: 4i5b  
  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, Nov 28, 2012
Title structure of human mhc class ii protein hla-dr1 carrying an hemagglutinin peptide partially filling the binding groove
Authors M.-S.E.D.SCHULZE
Method X-RAY DIFFRACTION (resolution: 2.12Å)
PDBe Citation   
Ligand bond colours:   *  covalent   *  ionic   *  hydrogen   *  electrostatic   *  van-der-waals   *  plane-atom   *  plane-plane   *  undefined  - Click here to show 5Å bonds
Chains A,D sequence:
KEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALANIACDKANLEIMTKRSNYTP
ITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVY
DCRVEHWGLDEPLLKHWEFDAPSPLPE
Chains B,E sequence:
DTRPRFLWQLKFECHFFNGTERVRLLERSIYNQEESVRFDSDVGEYRAVTELGRPDAEYWNSQKDLLEQRRAAVDTYCRH
NYGVGESFTVQRRVEPKVTVYPSKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNGDWTFQTLVML
ETVPRSGEVYTCQVEHPSVTSPLTVEWRARSE
Chains C,F sequence:
VVKQNCLKLATK
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: 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.hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..........eeeeee.........eeeeeeeeee.....eeeeee..ee.....ee...ee.....eeeeeeeee.......eeeeee.......eeeee...
sequence :  ..KEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALANIACDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEFD
seq num:  ..2         12        22        32        42        52        62        72        82        92        102       112       122       132       142       152       162       172       
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 ..                                                                    *****                                                                                 | |                       
search RasMol script viewer Motif-ligand binding stats  stturn ..                                                                                                                                                          ***                       

chain B : HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DRB1-1 B
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....eeeeeeeeee..eeeeeee.....eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeee.........eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeee......eeeeeee.......eeeeee....
sequence :  ..DTRPRFLWQLKFECHFFNGTERVRLLERSIYNQEESVRFDSDVGEYRAVTELGRPDAEYWNSQKDLLEQRRAAVDTYCRHNYGVGESFTVQRRVEPKVTVYPSKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSVTSPLTVEWRARSE
seq num:  ..2         12        22        32        42        52        62        72        82        92        102       112       122       132       142       152       162       172       182         
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 : TRUNCATED HEMAGGLUTININ PEPTIDE
sec str:  ..............
sequence :  ..VVKQNCLKLATK
seq num:  ..308         

Assembly 2     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 D : HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR ALPHA
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..hhhhhhhhhhhhhhhhhhhhhhh..........eeeeee.........eeeeeeeeee.....eeeeee..eee....ee...ee.....eeeeeeeee......eeeeeee.......eeeeee.........
sequence :  ..KEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALANIACDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEFDAPSPLPE
seq num:  ..2         12        22        32        42        52        62        72        82        92        102       112       122       132       142       152       162       172       182    
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  ststaple ..                                                                    *****                                                                                 | |                              
search RasMol script viewer Motif-ligand binding stats  stturn ..                                                                                                                                                          ***                              

chain E : HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DRB1-1 B
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....eeeeeeeeee..eeeeeee.....eee.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeee.........eeeeeeeeee.....eeeeee..ee....eee...ee.....eeeeeeeee......eeeeeee.......eeeeee..
sequence :  ..DTRPRFLWQLKFECHFFNGTERVRLLERSIYNQEESVRFDSDVGEYRAVTELGRPDAEYWNSQKDLLEQRRAAVDTYCRHNYGVGESFTVQRRVEPKVTVYPSKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSVTSPLTVEWRAR
seq num:  ..2         12        22        32        42        52        62        72        82        92        102       112       122       132       142       152       162       172       182       
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 F : TRUNCATED HEMAGGLUTININ PEPTIDE
sec str:  .............
sequence :  ..VVKQNCLKLAT
seq num:  ..308        

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