triangle PDBeMotif: 2xtj  
  coner Sequences coner   coner 3D motifs coner   coner Ligand environment coner   coner Ligand bonds coner
   
coner
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Enzyme   3.4.21.
Classification hydrolase/antibody    | release date: Sun, Oct 10, 2010
Title the crystal structure of pcsk9 in complex with 1d05 fab
Authors A.CARFI, C.VOLPARI, S.DI MARCO
Method X-RAY DIFFRACTION (resolution: 2.70Å)
PDBe Citation   
Small molecules:    search CA CA binding statistics CA
Ligand bond colours:   *  covalent   *  ionic   *  hydrogen   *  electrostatic   *  van-der-waals   *  plane-atom   *  plane-plane   *  undefined  - Click here to show 5Å bonds
Chain A sequence:
SIPWNLERITPPRYRADEYQPPDGGSLVEVYLLDTSIQSDHREIEGRVMVTDFENVPEEDGTRFHRQASKCDSHGTHLAG
VVSGRDAGVAKGASMRSLRVLNCQGKGTVSGTLIGLEFIRKSQLVQPVGPLVVLLPLAGGYSRVLNAACQRLARAGVVLV
TAAGNFRDDACLYSPASAPEVITVGATNAQDQPVTLGTLGTNFGRCVDLFAPGEDIIGASSDCSTCFVSQSGTSQAAAHV
AGIAAMMLSAEPELTLAELRQRLILFSAKDVINEAWFPEDQRVLTPNLVAALPPSTHGAAGTAAASHHHHHH
Chain P sequence:
MKGSKGSKGSKPMSAEAPEHGTTATFHRCAKDPWRLPGTYVVVLKEETHLSQSERTARRLQAQAARRGYLTKILHVFHGL
LPGFLVKMSGDLLELALKLPHVDYIEEDSSVFAQ
Chain B sequence:
DIQMTQSPSSLSASVGDRVTITCRASQGIRSALNWYQQKPGKAPKLLIYNGSTLQSGVPSRFSGSGSGTDFTLTISSLQP
EDFAVYYCQQFDGDPTFGQGTKVEIKR
Chain C sequence:
TVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEK
HKVYACEVTHQGLSSPVTKSFNRGEA
Chain D sequence:
QVQLVQSGAEVKKPGSSVKVSCKASGGTFNSHAISWVRQAPGQGLEWMGGINPILGIANYAQKFQGRVTITADESTSTAY
MELSSLRSEDTAVYYCARHYEIQIGRYGMNVYYLMYRFASWGQGTLVTVSS
Chain E sequence:
ASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQT
YICNVNHKPSNTKVDKKVEPKSEFEQKLISEEDLNGAPHHHHHH
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 : PROPROTEIN CONVERTASE SUBTILISIN/KEXIN TYPE 9
member of: CATH:search3.40.50.200GENE3D:searchG3DSA_3.30.70.80/searchG3DSA_3.40.50.200PANTHER:searchPTHR10795/searchPTHR10795_SF333PFAM:searchPF00082PRINTS:searchSUBTILISINSUPERFAMILY:searchSSF52743UniProt:searchQ8NBP7
JMol viewer RasMol script viewer  CA 1423A  ..   ..                                   ..                                                                                                               *  * *                        *                                                              
sec str:  ..........eeeeee.............eeeeeee.............hhhhhhhhhhhhh..........eeeee......eeehhhhhhhhhhhhhhhhhh....eeeee.eeee.hhhhhhhhhhhhhh..eeeee..........ee.......eeeeee.....................eeee...eeee......eeeee.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh...
sequence :  ..PWN..SLVEVYLLDTSIQSDHREIEGRVMVTDFENVPEED..QASKCDSHGTHLAGVVSGRDAGVAKGASMRSLRVLNCQGKGTVSGTLIGLEFIRKSQLVQPVGPLVVLLPLAGGYSRVLNAACQRLARAGVVLVTAAGNFRDDACLYSPASAPEVITVGATNAQDQPVTLGTLGTNFGRCVDLFAPGEDIIGASSDCSTCFVSQSGTSQAAAHVAGIAAMMLSAEPELTLAELRQRLILFSAKD
seq num:  ..155..178       188       198       208  ..219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419 
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  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  schellmannloop ..   ..        |                | |       ..     | | |                                                                           ******       |                                                      | |           |                    |   |           
search RasMol script viewer Motif-ligand binding stats  stmotif ..   ..        |                | |       ..     | | |                                                                                        |                                                      | |           |                    *****           
search RasMol script viewer Motif-ligand binding stats  ststaple ..   ..        |                | |       ..     *****                                                                                        |                                                      | |           |                                    
search RasMol script viewer Motif-ligand binding stats  stturn ..   ..        |                ***       ..       |                                                                                          |                                                      ***           |                                    
search RasMol script viewer Motif-ligand binding stats  Catalytic site ..   ..        *                          ..       *                                                                                          *                                                                    *                                    

chain B : FAB FROM A HUMAN MONOCLONAL ANTIBODY, 1D05
member of: CATH:search2.60.40.10
sec str:  .....eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee.....ee...eeeee..
sequence :  ..DIQMTQSPSSLSASVGDRVTITCRASQGIRSALNWYQQKPGKAPKLLIYNGSTLQSGVPSRFSGSGSGTDFTLTISSLQPEDFAVYYCQQFDGDPTFGQGTKVEIKR
seq num:  ..1         11        21        31        41        51        61        71        81        91        101    
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  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 C : FAB FROM A HUMAN MONOCLONAL ANTIBODY, 1D05
member of: CATH:search2.60.40.10
sec str:  .......eeeee..hhhhhhhheeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee...
sequence :  ..TVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE
seq num:  ..108       118       128       138       148       158       168       178       188       198       208  
search RasMol script viewer Motif-ligand binding stats  CK2_PHOSPHO_SITE ..            |   | | |           | |      |  |   | |  ^*** | || |         ^***|  |  | |   |  |            
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  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 D : FAB FROM A HUMAN MONOCLONAL ANTIBODY, 1D05
member of: CATH:search2.60.40.10
sec str:  ....eeee...eee.....eeeeeeee.......eeeeeee......eeeeeee....eeee.hhhh..eeeeee....eeeeee...hhhhheeeeeeeeeeee.......eeeee.........eeeee..
sequence :  ..QVQLVQSGAEVKKPGSSVKVSCKASGGTFNSHAISWVRQAPGQGLEWMGGINPILGIANYAQKFQGRVTITADESTSTAYMELSSLRSEDTAVYYCARHYEIQIGRYGMNVYYLMYRFASWGQGTLVTVSS
seq num:  ..1         11        21        31        41        51        61        71        81        91        101       111       121        
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  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 ..                       ******                                *******              **** ****           ******                       

chain E : FAB FROM A HUMAN MONOCLONAL ANTIBODY, 1D05
sec str:  ........eeeee......ee..eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee........
sequence :  ..ASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSEFE
seq num:  ..132       142       152       162       172       182       192       202       212       222       232  
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  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 P : PROPROTEIN CONVERTASE SUBTILISIN-KEXIN TYPE 9
member of: GENE3D:searchG3DSA_3.30.70.80PANTHER:searchPTHR10795/searchPTHR10795_SF333PFAM:searchPF05922SUPERFAMILY:searchSSF52743/searchSSF54897UniProt:searchQ8NBP7
sec str:  ....eee...hhh.eeeeeeeeee....hhhhhhhhhhhhhhhhhh.....eeeeee.....eeeee.hhhhhhhhh....eeeeeeeeeeee.
sequence :  ..TATFHRCAKDPWRLPGTYVVVLKEETHLSQSERTARRLQAQAARRGYLTKILHVFHGLLPGFLVKMSGDLLELALKLPHVDYIEEDSSVFAQ
seq num:  ..61        71        81        91        101       111       121       131       141         
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  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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