triangle PDBeMotif: 3pgd  
  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: Mon, Nov 1, 2010
Title crystal structure of hla-dr1 with clip106-120, canonical pep orientation
Authors A.SCHLUNDT, C.FREUND, G.JUNG, J.STICHT, K.-H.WIESM, K.FALK, O.ROTZSCHKE, S.GUNTHER, U.HEINEMANN, Y.ROSKE
Method X-RAY DIFFRACTION (resolution: 2.72Å)
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:
MIKEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALANIAVDKANLEIMTKRSNY
TPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTED
VYDCRVEHWGLDEPLLKHWEFDAPSPLPETTEN
Chains B,E sequence:
MGDTRPRFLWQLKFECHFFNGTERVRLLERCIYNQEESVRFDSDVGEYRAVTELGRPDAEYWNSQKDLLEQRRAAVDTYC
RHNYGVGESFTVQRRVEPKVTVYPSKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNGDWTFQTLV
MLETVPRSGEVYTCQVEHPSVTSPLTVEWRARSESAQSK
Chains C,F sequence:
KMRMATPLLMQALPM
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
sec str:  ...eeeeeeeeeee...eeeeeeee..eeeeeee....eeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh..........eeeeee.........eeeeeeeeee.....eeeeee..eee....ee...ee.....eeeeeeeee.......eeeeee.......eeeee...
sequence :  ..EHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEFD
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  asxmotif ..          |  | |      |  |     *****|               |  |              || |||                  |  |       |  |          |  |  |  |       | |||           |  |       |  |           
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 ..                                                                      ******                                                                                                      

chain B : HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DRB1-1 B
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.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........eeeeeee.....eeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeee.......eeeeeee.......eeeeee.
sequence :  ..MGDTRPRFLWQLKFECHFFNGTERVRLLERCIYNQEESVRFDSDVGEYRAVTELGRPDAEYWNSQKDLLEQRRAAVDTYCRHNYGVGESFTVQRRVEPKVTVYPSKT..NLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSVTSPLTVEWRA
seq num:  ..0         10        20        30        40        50        60        70        80        90        100    ..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 C : HLA CLASS II HISTOCOMPATIBILITY ANTIGEN GAMMA CHA
member of: PANTHER:searchPTHR14093/searchPTHR14093_SF5PFAM:searchPF09307PIRSF:searchPIRSF001992PRINTS:searchCD74ANTIGENUniProt:searchP04233
sec str:  .................
sequence :  ..KMRMATPLLMQALPM
seq num:  ..106       116  
search RasMol script viewer Motif-ligand binding stats  niche ..          ***  

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: 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:  ...eeeeeeeeeeee...eeeeeeee..eeeeeee....eeee.hhhhhhh....hhhhhhhhhhhhhhhhhhhhhh..........eeeeee.........eeeeeeeeee.....eeeeee..eee....ee...ee.....eeeeeeeee.......eeeeee.......eeeee...
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  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 E : HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DRB1-1 B
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.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........eeeeeee.....eeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeee.......eeeeeee.......eeeeee.
sequence :  ..MGDTRPRFLWQLKFECHFFNGTERVRLLERCIYNQEESVRFDSDVGEYRAVTELGRPDAEYWNSQKDLLEQRRAAVDTYCRHNYGVGESFTVQRRVEPKVTVYPSKT..NLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSVTSPLTVEWRA
seq num:  ..0         10        20        30        40        50        60        70        80        90        100    ..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 F : HLA CLASS II HISTOCOMPATIBILITY ANTIGEN GAMMA CHA
member of: PANTHER:searchPTHR14093/searchPTHR14093_SF5PFAM:searchPF09307PIRSF:searchPIRSF001992PRINTS:searchCD74ANTIGENUniProt:searchP04233
sec str:  .................
sequence :  ..KMRMATPLLMQALPM
seq num:  ..106       116  

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