triangle PDBeMotif: 1t5w  
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Classification immune system    | release date: Wed, May 5, 2004
Title hla-dr1 in complex with a synthetic peptide (aaysdqatplllspr)
Authors I.STRUG, J.GORSKI, L.J.STERN, M.W.ANDERSON, Z.ZAVALA-RUIZ
Method X-RAY DIFFRACTION (resolution: 2.40Å)
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:
KEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALANIAVDKANLEIMTKRSNYTP
ITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVY
DCRVEHWGLDEPLLKHWEFD
Chains B,E sequence:
GDTRPRFLWQLKFECHFFNGTERVRLLERCIYNQEESVRFDSDVGEYRAVTELGRPDAEYWNSQKDLLEQRRAAVDTYCR
HNYGVGESFTVQRRVEPKVTVYPSKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNGDWTFQTLVM
LETVPRSGEVYTCQVEHPSVTSPLTVEWRA
Chains C,F sequence:
AAYSDQATPLLLSPR
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: 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.hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh..........eeeeee.........eeeeeeeeee.....eeeeee..eee....ee...ee.....eeeeeeeee.......eeeeee.......eeeee...
sequence :  ..KEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEFD
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  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, DRB1-1BETA CHAIN;
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....eeeeeeeee....eeeeee.....eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........eeeeeee........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  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 : 15-MER PEPTIDE FRAGMENT OF REGULATORY PROTEINMIG1;
member of: UniProt:searchP27705
sec str:  ...............
sequence :  ..AAYSDQATPLLLS
seq num:  ..0         10 
search RasMol script viewer Motif-ligand binding stats  PKC_PHOSPHO_SITE ..            ^

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, DRALPHA CHAIN;
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.hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh..........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  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 E : HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DRB1-1BETA CHAIN;
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....eeeeeeeee....eeeeee.....eee.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeeee........eeeeeeeeee.....eeeeee..eee...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 .. | |                                    **** |             ****|        ****         |   ****              |  |       |  | | |      **** ||| | | |   |||||           ****       |  | |        
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chain F : 15-MER PEPTIDE FRAGMENT OF REGULATORY PROTEINMIG1;
member of: UniProt:searchP27705
sec str:  ...............
sequence :  ..AAYSDQATPLLLS
seq num:  ..0         10 
search RasMol script viewer Motif-ligand binding stats  PKC_PHOSPHO_SITE ..            ^

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