triangle PDBeMotif: 3l9j  
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Classification immune system    | release date: Tue, Jan 5, 2010
Title selection of a novel highly specific tnfalpha antagonist: in the crystal structure of the antagonist-tnfalpha complex
Authors H.C.THOGERSEN, H.H.GAD, M.H.ANDERSEN, P.BYLA, R.HARTMANN
Method X-RAY DIFFRACTION (resolution: 2.10Å)
PDBe Citation   
Small molecules:    search MG MG binding statistics MG
Ligand bond colours:   *  covalent   *  ionic   *  hydrogen   *  electrostatic   *  van-der-waals   *  plane-atom   *  plane-plane   *  undefined  - Click here to show 5Å bonds
Chain C sequence:
LQTVCLKGTKHMKCFLAFTQTKTFHEASEDCISRGGTLSTPQTGSENDALYEYLRQSVGNEAEIWLGLNKRWSRYFWVDM
TGTRIAYKNWEHSSDAQPDPSNWENCAVLSGAANGKWFGKRCRDQLPYICQFGI
Chain T sequence:
SDKPVAHVVANPQAEGQLQWLNRRANALLANGVELRDNQLVVPSEGLYLIYSQVLFKGQGCPSTHVLLTHTISRIAVSYQ
TKVNLLSAIKSPCQRETPEGAEAKPWYEPIYLGGVFQLEKGDRLSAEINRPDYLDFAESGQVYFGIIAL
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 C : TNFALPHA
member of: CATH:search3.10.100.10GENE3D:searchG3DSA_3.10.100.10PANTHER:searchPTHR22799/searchPTHR22799_SF3PFAM:searchPF00059PRINTS:searchPNCREATITSAPPROSITE PATTERNS:searchPS00615, PROSITE PROFILES:searchPS50041, SMART:searchSM00034SUPERFAMILY:searchSSF56436/searchSSF57944UniProt:searchP05452
JMol viewer RasMol script viewer  MG 497C  ..      ..                                                                                                                            
sec str:  .....eee...eeeeeeeeeeehhhhhhhhhhhh..ee....hhhhhhhhhhhhhhhh....eee..ee........ee............hhhhhh........eeeee......eeee.....eeeeeeeee
sequence :  ..LQTVCL..HMKCFLAFTQTKTFHEASEDCISRGGTLSTPQTGSENDALYEYLRQSVGNEAEIWLGLNKRWSRYFWVDMTGTRIAYKNWEHSSDAQPDPSNWENCAVLSGAANGKWFGKRCRDQLPYICQFGI
seq num:  ..46    ..57        67        77        87        97        107       117       127       137       147       157       167       177 
search RasMol script viewer Motif-ligand binding stats  CAMP_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  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 ..      ..                                          *****                                                                             

chain T : TUMOR NECROSIS FACTOR, SOLUBLE FORM
member of: CATH:search2.60.120.40GENE3D:searchG3DSA_2.60.120.40PANTHER:searchPTHR11471/searchPTHR11471_SF23PFAM:searchPF00229PRINTS:searchTNECROSISFCT/searchTNFALPHAPROSITE PATTERNS:searchPS00251, PROSITE PROFILES:searchPS50049, SMART:searchSM00207SUPERFAMILY:searchSSF49842UniProt:searchP01375
sec str:  ......eeeeee.........ee......eee...eee..eee....eeeeeeeeeeeeee........eeeeeeee......eeeeeeeee..............eeeeeeeeeeeeee....eeeeee.hhhhh........eeeeee.
sequence :  ..SDKPVAHVVANPQAEGQLQWLNRRANALLANGVELRDNQLVVPSEGLYLIYSQVLFKGQGCPSTHVLLTHTISRIAVSYQTKVNLLSAIKSPCQRETPEGAEAKPWYEPIYLGGVFQLEKGDRLSAEINRPDYLDFAESGQVYFGIIAL
seq num:  ..9         19        29        39        49        59        69        79        89        99        109       119       129       139       149      
search RasMol script viewer Motif-ligand binding stats  PKC_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  nest ..| |       |  |  |      |  |                                  | |           | |                   |  |                 |  |        |  |     ***       
search RasMol script viewer Motif-ligand binding stats  niche ..| |       *******      ****                                  ***           ***                   ****                 ****        ****               
search RasMol script viewer Motif-ligand binding stats  stturn ..***                                                                                                                                                  

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