triangle PDBeMotif: 3pgc  
  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, flipped pepti 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: 2.66Å)
PDBe Citation   
Small molecules:    search PEG PEG binding statistics PEG   search GOL GOL binding statistics GOL
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.hhhhhh.ee..hhhhhhhhhhhhhhhhhhhhhh..........eeeeee.........eeeeeeeeee.....eeeeee..eee....ee...ee.....eeeeeeeee.......eeeeee.......eeeee..
sequence :  ..EHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEF
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  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, DRB1-1 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.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........eeeeee....eeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeee........eeeeee.......eeeee....
sequence :  ..GDTRPRFLWQLKFECHFFNGTERVRLLERCIYNQEESVRFDSDVGEYRAVTELGRPDAEYWNSQKDLLEQRRAAVDTYCRHNYGVGESFTVQRRVEPKVTVYPS..NLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSVTSPLTVEWRARS
seq num:  ..1         11        21        31        41        51        61        71        81        91        101 ..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  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 : HLA CLASS II HISTOCOMPATIBILITY ANTIGEN GAMMA CHA
member of: PANTHER:searchPTHR14093/searchPTHR14093_SF5PFAM:searchPF09307PIRSF:searchPIRSF001992PRINTS:searchCD74ANTIGENUniProt:searchP04233
sec str:  ............ee...
sequence :  ..KMRMATPLLMQALPM
seq num:  ..106       116  

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
JMol viewer RasMol script viewer  GOL 194D  ..                                         ***                                                                                                                                      
JMol viewer RasMol script viewer  PEG 193D  ..*                                        |||                                                                                                                                      
sec str:  ...eeeeeeeeeee...eeeeeeee..eeeeeee....eeee...hhhhhee.hhhhhhhhhhhhhhhhhhhhhhh..........eeeeee.........eeeeeeeeee.....eeeeee..eee....ee...ee.....eeeeeeeee......eeeeeee.......eeeeee..
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  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 ..                                             ****                                             ****                           ****                       ****       ****           

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
JMol viewer RasMol script viewer  GOL 194D  ..                                                                                           *           ..                                                                             
JMol viewer RasMol script viewer  PEG 193D  ..                *                                                                          |           ..                                                                             
sec str:  .......eeeeeeeeeeee....eeeeeeeeee..eeeeeee.....eee.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeee....eeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeee........eeeeee.......eeeee.
sequence :  ..DTRPRFLWQLKFECHFFNGTERVRLLERCIYNQEESVRFDSDVGEYRAVTELGRPDAEYWNSQKDLLEQRRAAVDTYCRHNYGVGESFTVQRRVEPKVTVYPS..NLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSVTSPLTVEWR
seq num:  ..2         12        22        32        42        52        62        72        82        92           ..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  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 ..                                                                                        ****           ..      **** ***           *****                       ****       ******       

chain F : HLA CLASS II HISTOCOMPATIBILITY ANTIGEN GAMMA CHA
member of: PANTHER:searchPTHR14093/searchPTHR14093_SF5PFAM:searchPF09307PIRSF:searchPIRSF001992PRINTS:searchCD74ANTIGENUniProt:searchP04233
sec str:  ............ee...
sequence :  ..KMRMATPLLMQALPM
seq num:  ..106       116  

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