triangle PDBeMotif: 3t0e  
  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, Jul 20, 2011
Title crystal structure of a complete ternary complex of t cell re peptide-mhc and cd4
Authors R.A.MARIUZZA, Y.YIN
Method X-RAY DIFFRACTION (resolution: 4.00Å)
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:
IKEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALANIAVDKANLEIMTKRSNYT
PITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDV
YDCRVEHWGLDEPLLKHWEFDA
Chain B sequence:
FSWGAEGQRPGFGSGGGSLVPRGSGGGGSGDTRPRFLEQVKHECHFFNGTERVRFLDRYFYHQEEYVRFDSDVGEYRAVT
ELGRPDAEYWNSQKDLLEQKRAAVDTYCRHNYGVGESFTVQRRVYPEVTVYPAKTQPLQHHNLLVCSVNGFYPGSIEVRW
FRNGQEEKTGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSLTSPLTVEWRARS
Chain C sequence:
GDAKTTQPNSMESNEEEPVHLPCNHSTISGTDYIHWYRQLPSQGPEYVIHGLTSNVNNRMASLAIAEDRKSSTLILHRAT
LRDAAVYYCTVYGGATNKLIFGTGTLLAVQPNIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKTV
LDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPSPESSC
Chain D sequence:
VVSQHPSWVIAKSGTSVKIECRSLDFQATTMFWYRQFPKQSLMLMATSNEGSKATYEQGVEKDKFLINHASLTLSTLTVT
SAHPEDSSFYICSARGGSYNSPLHFGNGTRLTVTEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWW
VNGKEVHSGVSTDPQPLKEQPALNDSRYSLSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAW
GRADC
Chain E sequence:
KKVVLGKKGDTVELTCTASQKKSIQFHWKNSNQIKILGNYGSFLWKGPSKLNDRADSRRSLWDQGNFPLIIKNLKIEDSD
TYICEVEDQKEEVQLLVFGLTANSDTHLLQGQSLTLTLESPPGSSPSVQCRSPRGKNIQGGKTLSVSQLELQDSGTWTCT
VLQNQKKVEFKIDIVVLAFQKASSIVYKKEGEQVEFSFPLAFTVEKLTGSGELWWQAERASSSKSWITFDLKNKEVSVKR
VTQDPKLQMGKKLPLHLTLPQALPQYAGSGNLTLALEAKTGKLHQEVNLVVMRATQLQKNLTCEVWGPTSPKLMLSLKLE
NKEAKVSKREKAVWVLNPEAGMWQCLLSDSGQVLLESNIKVLPAADYKDDDDK
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_SF47PFAM:searchPF00993/searchPF07654PROSITE PATTERNS:searchPS00290, PROSITE PROFILES:searchPS50835, SMART:searchSM00407/searchSM00920SUPERFAMILY:searchSSF48726/searchSSF54452UniProt:searchP01903
sec str:  .....eeeeeeeee...eeeeeeee..eeeee...........hhhhh......hhhhhhhhhhhhhhhhhhhhhh..........eeeeee.........eeeeeeeeee.....eeeeee..ee.....eeeeeee.....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  alphabetamotif ..             | |                  | |     |  |  | |                 *****| |                  |  |       |  |          |  |               | |         | |          |  |           
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 ..                                                                                              ****       ****                                                      ****           

chain B : HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DRB1-4 B
member of: CATH:search2.60.40.10/search3.10.320.10GENE3D:searchG3DSA_2.60.40.10/searchG3DSA_3.10.320.10PANTHER:searchPTHR19944/searchPTHR19944_SF57PFAM:searchPF00969/searchPF07654PRODOM:searchPD000328PROSITE PATTERNS:searchPS00290, PROSITE PROFILES:searchPS50835, SMART:searchSM00407/searchSM00921SUPERFAMILY:searchSSF48726/searchSSF54452UniProt:searchP13760
sec str:  .........................eeeeeee..ee......ee.eeeeee...eeeeee.....eee....hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..........ee........eeeeee.......eeeeee..ee....eee...ee.....eeeeeee.........eeeeee.......eeeee.
sequence :  ..FSWGAEGQRPGFGSGG..DTRPRFLEQVKHECHFFNGTERVRFLDRYFYHQEEYVRFDSDVGEYRAVTELGRPDAEYWNSQKDLLEQKRAAVDTYCRHNYGVGESFTVQRRVYPEVTVYPA..LLVCSVNGFYPGSIEVRWFRNGQEEKTGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSLTSPLTVEWR
seq num:  ..1         11    ..31        41        51        61        71        81        91        101       111       121          ..143       153       163       173       183       193       203       213   
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  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  stturn ..                ..                                                                                                       ..                              ***                                           

chain C : T-CELL RECEPTOR ALPHA CHAIN
member of: CATH:search2.60.40.10GENE3D:searchG3DSA_2.60.40.10PANTHER:searchPTHR19433/searchPTHR19433_SF65PFAM:searchPF09291SUPERFAMILY:searchSSF48726UniProt:searchP01848
sec str:  .........eeeee....eeeeee........eeeeeee.....eeeeeee...eeee..eeeee.....eeeeee...hhhhheeeeeeee............eeeeee........eee..ee.........eee...............eee...eeeee....eeeeeeeeee............ ...........
sequence :  ..AKTTQPNSMESNEEEPVHLPCNHSTISGTDYIHWYRQLPSQGPEYVIHGLTSNVNNRMASLAIAEDRKSSTLILHRATLRDAAVYYCTVYGGATNKLIFGTGTLLAVQPNIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKTVLDMRSMDFKSNSAVAWSNKSDFACAN... ..NSIIPEDTF
seq num:  ..1         11        21        31        41        51        61        71        81        91        101       111       121       131       141       151       161       171       181 ... ..188      
search RasMol script viewer Motif-ligand binding stats  ASN_GLYCOSYLATION ..          || ||      ^*** |  |                  |    |         | |||||       |||||        |  | |     |    |     | |         |||||| |  |  |  |^***  ||||  | ||  ||| |||        |^***|    ..PS00001..***      
search RasMol script viewer Motif-ligand binding stats  CAMP_PHOSPHO_SITE ..          || ||           |  |                  |    |         | |**^*       |||||        |  | |     |    |     | |         |||||| |  |  |  |      ||||  | ||  ||| |||        | || |    ..PS00004..         
search RasMol script viewer Motif-ligand binding stats  PKC_PHOSPHO_SITE ..          || ||           |  |                  |    |         | ||||        ^**||        |  ^**     |    |     | |         ||^**| |  |  |  |      ||||  ^**|  ||| |||        ^**| |    ..PS00005..         
search RasMol script viewer Motif-ligand binding stats  CK2_PHOSPHO_SITE ..          ^***|           ^***                  |    |         | ||||        ^***|        |  | |     |    |     | |         |||| | |  ^***  |      ||||     ^***|| |||           | |    ..PS00006..         
search RasMol script viewer Motif-ligand binding stats  MYRISTYL ..           |  |                                 ^*****         | ||||         |  |        ^*****     ^*****     | |         |||| | |     |  |      ||||         || |||           | |    ..PS00008..         
search RasMol script viewer Motif-ligand binding stats  asxturn ..           |  |                                                | ***|         |  |        |  | |                | |         |||| | |     |  |      ||||         || |||           | |    ..asxturn..         
search RasMol script viewer Motif-ligand binding stats  betaturn ..           ****                                                ****||         |  |        |  | |                | |         |||| | |     |  |      ||||         |****|           | |    ..betaturn..         
search RasMol script viewer Motif-ligand binding stats  gammaturn ..           |  |                                                  ||||         |  |        |  | |                ***         |||| | |     |  |      ||||         |  | |           | |    ..gammaturn..         
search RasMol script viewer Motif-ligand binding stats  nest ..           |  |                                                  ****         |  |        |  | |                            **** | |     |  |      ****         |  ***           | |    ..nest..         
search RasMol script viewer Motif-ligand binding stats  niche ..           ****                                                               ****        ******                                 ***     ****                   |    |           ***    ..niche..         
search RasMol script viewer Motif-ligand binding stats  schellmannloop ..                                                                                                                                                                ******                  ..schellmannloop..         

chain D : T-CELL RECEPTOR BETA CHAIN
member of: CATH:search2.60.40.10GENE3D:searchG3DSA_2.60.40.10PANTHER:searchPTHR23268/searchPTHR23268_SF15PFAM:searchPF07654PROSITE PROFILES:searchPS50835, SMART:searchSM00407SUPERFAMILY:searchSSF48726UniProt:searchA0A5B9
sec str:  ...eeee..ee.......eeeeeee......eeeeeee......eeeeeee.....ee....hhh.eee.......eeeee...hhhhheeeeeeee.......ee....eee....hhhhh...eeeeee.hhhhhhhhheee.eeeeeee....eeeeeee..ee....eee....ee.........eeeeeeeeee.hhhh....eeeeeeee..................eeeeeeee.....
sequence :  ..VVSQHPSWVIAKSGTSVKIECRSLDFQATTMFWYRQFPKQSLMLMATSNEGSKATYEQGVEKDKFLINHASLTLSTLTVTSAHPEDSSFYICSARGGSYNSPLHFGNGTRLTVTEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVSTDPQPLKEQPALNDSRYSLSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRADC
seq num:  ..1         11        21        31        41        51        61        71        81        91        101       111       121       131       141       151       161       171       181       191       201       211       221       231       241  
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  MYRISTYL ..                                      | |         ^*****|  | |  | | |              |  |        ^*****      ^*****   |  |                 | |           | |            |  |                          | ||||| ||         ^*****       | |              
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  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  stturn ..                                                                                                                                         ***                                                                                                         

chain E : T-CELL SURFACE GLYCOPROTEIN CD4
member of: CATH:search2.60.40.10GENE3D:searchG3DSA_1.20.5.900/searchG3DSA_2.60.40.10PANTHER:searchPTHR11422/searchPTHR11422_SF0PFAM:searchPF05790/searchPF07686/searchPF09191PRINTS:searchCD4TCANTIGENPROSITE PROFILES:searchPS50835, SMART:searchSM00406/searchSM00409SUPERFAMILY:searchSSF48726UniProt:searchP01730
sec str:  .....eeee....eee...........eeeee...eeeeeee..eeee....hhh.ee.hhhhhh.....eee...hhhhheeeeeee.....eeeeeeeeee............eeeeee..........ee.....ee....eeee...hhhhh..eeeeeee..eeeeeee............eeee.....................eeeee.............ee.........................................eeeee............eeeeee.........eee.........eee........eee...ee...........ee...................
sequence :  ..KKVVLGKKGDTVELTCTASQKKSIQFHWKNSNQIKILGNYGSFLWKGPSKLNDRADSRRSLWDQGNFPLIIKNLKIEDSDTYICEVEDQKEEVQLLVFGLTANSDTHLLQGQSLTLTLESPPGSSPSVQCRSPRGKNIQGGKTLSVSQLELQDSGTWTCTVLQNQKKVEFKIDIVVLAFQKASSIVYKKEGEQVEFSFPLAFTVEKLTGSGELWWQAERASSSKSWITFDLKNKEVSVKRVTQDPKLQMGKKLPLHLTLPQALPQYAGSGNLTLALEAKTGKLHQEVNLVVMRATQLQKNLTCEVWGPTSPKLMLSLKLENKEAKVSKREKAVWVLNPEAGMWQCLLSDSGQVLLESNIKVLPAA
seq num:  ..1         11        21        31        41        51        61        71        81        91        101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361  
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  TYR_PHOSPHO_SITE ..    | || |                           | || |   | | || ||        | |        *******^      | |       |    | |  | ||   |    | ||   |     | |             || |||    |             | |            |  |        | |                    |||||   |  || || |       | ||           |  |        | | | ||         | | || | |       ||||    | |   | |              |    |  | |              
search RasMol script viewer Motif-ligand binding stats  MYRISTYL ..    | || |                           ^*****   | | || ||        | |         |  |         | |       ^***** |  | ^*****    | ^*****     | |             || ||^*****             | |            |  |        | |                    |||||   |  || || |       | ||           |  |        | | | ||         | | || | |       ||||    | |   | |              ^*****  | |              
search RasMol script viewer Motif-ligand binding stats  AMIDATION ..    ^*** |                             || |   | | || ||        | |         |  |         | |            | |  |  |        |  |         | |             || ||                   | |            |  |        | |                    |||||   |  || || |       ^***           |  |        | | | ||         | | || | |       ||||    | |   | |                      | |              
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  stturn ..                                                ***                                                                                                                                                                                                                                                                                                                          

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