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Classification immune system/viral protein    | release date: Tue, Sep 9, 2014
Title structure of the core ectodomain of the hepatitis c virus en glycoprotein 2
Authors A.A.PRICE, A.CY, A.G.KHAN, A.GRAKOUI, A.V.ZATORSKI, C.D.BOHANNON, H.SCARBOROUGH, J.JACOB, J.MARCOTR, J.WHIDBY, M.T.MILLER, S.A.YOST
Method X-RAY DIFFRACTION (resolution: 2.40Å)
PDBe Citation   
Small molecules:    search NAG NAG binding statistics NAG   search ARF ARF binding statistics ARF
Ligand bond colours:   *  covalent   *  ionic   *  hydrogen   *  electrostatic   *  van-der-waals   *  plane-atom   *  plane-plane   *  undefined  - Click here to show 5Å bonds
Chain E sequence:
TPVGLAMSACRSIEAFRVGWGALQYEDNVTNPEDMRPYCWHYPPRQCGVVSAKTVCGPVYCFTPSPVVVGTTDRLGAPTY
TWGENETDVFLLNSTRPPLGSWFGCTWMNSSGYTKTCGAPPCRTRADFNASTDLLCPTDCFRKHPDTTYLKCGSGPWLTP
RCLIDYPYRLWHYPCTVNYTIFKIRMYVGGVEHRLTAACNFTRGDRGSASGLEVLFQ
Chain H sequence:
MKCSWVIFFLMAVVTGVISEVQLQQSGAELVKPGASVKLSCTASGFNIKDTYIHWVNQRPEQGLEWIGRIDPANGHTQYD
PKFQGKATITADTSSNTAYLQLSSLTSEDTAVYYCATSDYSYALDSWGQGTSVTVSSAKTTAPSVYPLAPVCGDTTGSSV
TLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRGPT
IKPCPPCKCPAPNLLGGPSVFIFPPKIKDVLMISLSPIVTCVVVDVSEDDPDVQISWFVNNVEVHTAQTQTHREDYNSTL
RVVSALPIQHQDWMSGKEFKCKVNNKDLPAPIERTISKPKGSVRAPQVYVLPPPEEEMTKKQVTLTCMVTDFMPEDIYVE
WTNNGKTELNYKNTEPVLDSDGSYFMYSKLRVEKKNWVERNSYSCSVVHEGLHNHHTTKSFSRTPGK
Chain L sequence:
MESQTQVLMFLLLWVSGACADIVMTQSPSSLAMSVGQKVTMSCKSSQSLLNSNNQKNYLAWYQQKPGQSPKLLVYFASTR
ESGVPDRFIGSGSGTDFTLTISSVQAEDLADYFCQQHYSTPYTFGGGTKLEIRRADAAPTVSIFPPSSEQLTSGGASVVC
FLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC
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 E : HEPATITIS C VIRUS ENVELOPE GLYCOPROTEIN 2
member of: PFAM:searchPF01560UniProt:searchQ9QF35
JMol viewer RasMol script viewer  ARF 703E  ..                                   ..                                  ..                                      *      *        
JMol viewer RasMol script viewer  NAG 702E  ..                                   ..                                  ..                            *   *     |      |       *
JMol viewer RasMol script viewer  NAG 701E  ..                                   ..                    *** *         ..                            |   |     |      |       |
sec str:  ......................eeee...eeee.....................eeeee.....eeeee.......hhhhh..........ee...hhhhhhhhhh...eeeeeeee..eeeeeeee..
sequence :  ..CWHYPPRQCGVVSAKTVCGPVYCFTPSPVVVGTTD..VFLLNSTRPPLGSWFGCTWMNSSGYTKTCGAPPC..TTYLKCGSGPWLTPRCLIDYPYRLWHYPCTVNYTIFKIRMYVGGVEHRLTAACN
seq num:  ..488       498       508       518  ..538       548       558       568 ..596       606       616       626       636       646 
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  RGD ..            | |        |  |        ..  | |  |  |           | |         ..        | | |  |             |  |        |  |         
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 ..                       ****        ..  ***                             ..        *** ****             ****                     

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 H : MOUSE FAB HEAVY CHAIN
JMol viewer RasMol script viewer  ARF 301L  ..                                         *                                                                                           ..                                                                                   
JMol viewer RasMol script viewer  ARF 503H  ..                                         |                                                         * *                               ..                                                                                   
JMol viewer RasMol script viewer  ARF 502H  ..                                         |                                                *        | |          * *                  ..                                                                                   
JMol viewer RasMol script viewer  ARF 501H  ..                                         |                                                |        | |          | |                  ..                                 *                                                 
sec str:  ....eeee...eee.....eeeeeeee..hhhhheeeeeee......eeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeeee.......ee...eeeee........eeeee...........eeeeeeeeee.....eeee........eeeeeee.....eeeeeeeee..........eeeeeehhhheeeeee....
sequence :  ..EVQLQQSGAELVKPGASVKLSCTASGFNIKDTYIHWVNQRPEQGLEWIGRIDPANGHTQYDPKFQGKATITADTSSNTAYLQLSSLTSEDTAVYYCATSDYSYALDSWGQGTSVTVSSAKTTAPSVYPLAPVC..TTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR
seq num:  ..1         11        21        31        41        51        61        71        81        91        101       111       121          ..136       146       156       166       176       186       196       206          
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  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 ..            ****            ****                             ****                      ****          | |            ***              ..                          *******        ***          ****          |    |         
search RasMol script viewer Motif-ligand binding stats  schellmannloop ..                                                                                                     | |                             ..                                                                    ******         
search RasMol script viewer Motif-ligand binding stats  stturn ..                                                                                                     ***                             ..                                                                                   

chain L : MOUSE FAB LIGHT CHAIN
JMol viewer RasMol script viewer  ARF 302L  ..                                          * *     *                *                   *                                                                                                                                 
JMol viewer RasMol script viewer  ARF 301L  ..                                          | |     |                |                   |  *                 *                                                                                                            
JMol viewer RasMol script viewer  ARF 503H  ..                                          | |     |   *            |                   |  |                 |                                                                                                            
JMol viewer RasMol script viewer  ARF 501H  ..                                          | |     |   |            |                   |  |                 |                                                               *                                            
sec str:  .....eeee..eeee.....eeeeeee.............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee...........eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhhh..eeeeee.......eeeee..
sequence :  ..DIVMTQSPSSLAMSVGQKVTMSCKSSQSLLNSNNQKNYLAWYQQKPGQSPKLLVYFASTRESGVPDRFIGSGSGTDFTLTISSVQAEDLADYFCQQHYSTPYTFGGGTKLEIRRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR
seq num:  ..1         11        21        31        41        51        61        71        81        91        101       111       121       131       141       151       161       171       181       191       201       211    
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  betabulge ..             |  |          | ||  | |        |  |    **      |  ||  |                 |  |                                           | |           | |            |  |          | |         | |             |  | |        
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 ..             ****          ***              ****            ********                 ****                                                         ***            ****                      | |             ******        
search RasMol script viewer Motif-ligand binding stats  stturn ..                           ***                                                                                                                                                             ***                ***        

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