triangle PDBeMotif: 3wd5  
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Classification immune system    | release date: Thu, Jun 6, 2013
Title crystal structure of tnfalpha in complex with adalimumab fab
Authors S.HU, S.Y.LIANG, Y.J.GUO, Z.Y.LOU
Method X-RAY DIFFRACTION (resolution: 3.10Å)
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:
VRSSSRTPSDKPVAHVVANPQAEGQLQWLNDRANALLANGVELRDNQLVVPSEGLYLIYSQVLFKGQGCPSTHVLLTHTI
SRIAVSYQTKVNLLSAIKSPCQRETPEGAEAKPWYEPIYLGGVFQLEKGDRLSAEINRPDYLDFAESGQVYFGIIAL
Chain L sequence:
DIQMTQSPSSLSASVGDRVTITCRASQGIRNYLAWYQQKPGKAPKLLIYAASTLQSGVPSRFSGSGSGTDFTLTISSLQP
EDVATYYCQRYNRAPYTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQ
ESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE
Chain H sequence:
EVQLVESGGGLVQPGRSLRLSCAASGFTFDDYAMHWVRQAPGKGLEWVSAITWNSGHIDYADSVEGRFTISRDNAKNSLY
LDMNSLRAEDTAVYYCAKVSYLSTASSLDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTV
SWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKI
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 : TUMOR NECROSIS FACTOR
member of: GENE3D:searchG3DSA_2.60.120.40PANTHER:searchPTHR11471/searchPTHR11471_SF7PFAM:searchPF00229PRINTS:searchTNECROSISFCT/searchTNFALPHAPROSITE PATTERNS:searchPS00251, PROSITE PROFILES:searchPS50049, SMART:searchSM00207SUPERFAMILY:searchSSF49842UniProt:searchP01375
sec str:  .........eeeeee.........ee......eee...ee....ee....eeeeeeeeeeeeee........eeeeeeee......eeeeeeeee..............eeeeeeeeeeeeee....eeeeee.hhhhh...hhhh.eeeeeee
sequence :  ..RTPSDKPVAHVVANPQAEGQLQWLNDRANALLANGVELRDNQLVVPSEGLYLIYSQVLFKGQGCPSTHVLLTHTISRIAVSYQTKVNLLSAIKSPCQRETPEGAEAKPWYEPIYLGGVFQLEKGDRLSAEINRPDYLDFAESGQVYFGIIAL
seq num:  ..6         16        26        36        46        56        66        76        86        96        106       116       126       136       146         
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  TNF_1 ..   | |                                    *****************                            ||       | || |                   |  |        |  ||  |           
search RasMol script viewer Motif-ligand binding stats  betabulge ..   | |                                                                                 **       | || |                   |  |        |  ||  |           
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  niche ..   ***                                                                                                                   ****        ********           

chain L : ADALIMUMAB LIGHT CHAIN
sec str:  .....eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......ee......eeeeee...hhhhh.eeeeee...........eeeee.......eeeee..hhhhhhhheeeeeeeeeee.....eeeeee..ee..................eeeeeeeeeehhhhh...eeeeeee.......eeeeee...
sequence :  ..DIQMTQSPSSLSASVGDRVTITCRASQGIRNYLAWYQQKPGKAPKLLIYAASTLQSGVPSRFSGSGSGTDFTLTISSLQPEDVATYYCQRYNRAPYTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE
seq num:  ..1         11        21        31        41        51        61        71        81        91        101       111       121       131       141       151       161       171       181       191       201          
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  betabulge ..             |  |           |  |      |  |    **      |  ||  |                || ||                                     |   | | |           | |      |  |                | |         |  ||  |        |  |            
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  stmotif ..                                                                                                                        *****                                                        *****                           

chain H : ADALIMUMAB HEAVY CHAIN
sec str:  ....eeeee..eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeee........eeee....eeee........eeeee.......eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee........eeeeeee....eee..ee
sequence :  ..EVQLVESGGGLVQPGRSLRLSCAASGFTFDDYAMHWVRQAPGKGLEWVSAITWNSGHIDYADSVEGRFTISRDNAKNSLYLDMNSLRAEDTAVYYCAKVSYLSTASSLDYWGQGTLVTVSSASTKGPSVFPLAPSS..GTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKI
seq num:  ..1         11        21        31        41        51        61        71        81        91        101       111       121       131   ..142       152       162       172       182       192       202       212     
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  asxturn ..                            |  |       |  |          ||||      ||| |    ***| |         |  |         | | |   ||         | |              ..                    |  | ||| |       | |||           | |  |          | |      
search RasMol script viewer Motif-ligand binding stats  betabulge ..                            |  |       |  |          ||||      ||| |       | |         |  |         | | |   **         | |              ..                    |  | ||| |       | |||           | |  |          | |      
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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