triangle PDBeMotif: 4nku  
  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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Enzyme   2.7.7.
Classification transferase/rna    | release date: Wed, Nov 13, 2013
Title structure of cid1 in complex with its short product apu
Authors C.GABUS, P.MUNOZ-TELLO, S.THORE
Method X-RAY DIFFRACTION (resolution: 1.94Å)
PDBe Citation   
Small molecules:    search MG MG binding statistics MG   search BR BR binding statistics BR
Ligand bond colours:   *  covalent   *  ionic   *  hydrogen   *  electrostatic   *  van-der-waals   *  plane-atom   *  plane-plane   *  undefined  - Click here to show 5Å bonds
Chains A,B sequence:
GDMSHKEFTKFCYEVYNEIKISDKEFKEKRAALDTLRLCLKRISPDAELVAFGSLESGLALKNSDMDLCVLMDSRVQSDT
IALQFYEELIAEGFEGKFLQRARIPIIKLTSDTKNGFGASFQCAIGFNNRLAIHNTLLLSSYTKLDARLKPMVLLVKHWA
KRKQINSPYFGTLSSYGYVLMVLYYLIHVIKPPVFPNLLLSPLKQEKIVDGFDVGFDDKLEDIPPSQNYSSLGSLLHGFF
RFYAYKFEPREKVVTFRRPDGYLTKQEKGWTSATEHTGSADQIIKDRYILAIEDPFEISHNVGRTVSSSGLYRIRGEFMA
ASRLLNSRSYPIPYDSLFEEA
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 : POLY(A) RNA POLYMERASE PROTEIN CID1
member of: GENE3D:searchG3DSA_1.10.1410.10/searchG3DSA_3.30.460.10PANTHER:searchPTHR12271PFAM:searchPF01909/searchPF03828SUPERFAMILY:searchSSF81301/searchSSF81631UniProt:searchO13833
JMol viewer RasMol script viewer  BR 101D  ..                                                                        ..                                                                             *                     *                                                                                             ..BR ..                                                       
JMol viewer RasMol script viewer  BR 403A  ..                                                                        ..                                                                             |                     |                                                             *                               ..BR ..                                                       
JMol viewer RasMol script viewer  MG 402A  ..                                                                        ..                                                                             |                     |                                                             |                               ..MG ..                                                       
JMol viewer RasMol script viewer  MG 401A  ..                                                                        ..                                                                             |                     |                                                             |                               ..MG ..                                                       
sec str:  .....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.....eeeeehhhhhh.......eeeeee.....hhhhhhhhhhhh.eeeee........eeeeee..........eeeee.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh...hhhhh..hhhhhhhhhhhhhhhh..................ee..ee.....hhhhh.......hhhhhhhhhhhhhhhh.................hhhhhh...... ......................hhhhhhhhhhhhhhhhhhhhh.....hhhhhhh..
sequence :  ..DMSHKEFTKFCYEVYNEIKISDKEFKEKRAALDTLRLCLKRISPDAELVAFGSLESGLALKNSDMDLCVLMD..TIALQFYEELIAEGFEGKFLQRARIPIIKLTSDTKNGFGASFQCAIGFNNRLAIHNTLLLSSYTKLDARLKPMVLLVKHWAKRKQINSPYFGTLSSYGYVLMVLYYLIHVIKPPVFPNLLLSPLKQEKIVDGFDVGFDDKLEDIPPSQNYSSLGSLLHGFFRFYAYKFEPREKVVTFRRPDGYLTKQEKGWTS... ..RYILAIEDPFEISHNVGRTVSSSGLYRIRGEFMAASRLLNSRSYPIPYDSLFEEA
seq num:  ..38        48        58        68        78        88        98          ..116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296          ... ..323       333       343       353       363       373  
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  alphabetamotif ..   |   |       |  |                   ***** ||         |||||  |         ..          | |||    |  |            ||||  |                     |  | |              |||||  | |                        ||| | |||   |  || |    |  |  | | |              | | |  |  | || |||     | |  ..alphabetamotif..          |  |  |  ||   |            |  | |      |  |  
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  nest ..   |   |       |  |                    |  | ||         ****|  |         ..            ***    |  |            ****  |                     |  |                ****   ***                         |  | |||       | |    |  |  | | |              | | |  |  | || ***     ***  ..nest..          |  |  |  ||   |            |  | |      |  |  
search RasMol script viewer Motif-ligand binding stats  niche ..   |   |       ****                    *******          *******         ..                   ****               ****                     ****                                                   *******|       ***    ****  *****              *** ****  ****              ..niche..          ****  ****|   |            ******      ****  
search RasMol script viewer Motif-ligand binding stats  stmotif ..   |   |                                  | |                           ..                                                                                                                         *****                    | |                          | |               ..stmotif..                    *****               | |            
search RasMol script viewer Motif-ligand binding stats  ststaple ..   *****                                  | |                           ..                                                                                                                         | |                      | |                          | |               ..ststaple..                                        | |            
search RasMol script viewer Motif-ligand binding stats  stturn ..                                          ***                           ..                                                                                                                         ***                      ***                          ***               ..stturn..                                        ***            

chain D : 5'-R(*AP*U)-3'
JMol viewer RasMol script viewer  BR 101D  .. *
sec str:  ....
sequence :  ..AU
seq num:  ..58

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 B : POLY(A) RNA POLYMERASE PROTEIN CID1
member of: GENE3D:searchG3DSA_1.10.1410.10/searchG3DSA_3.30.460.10PANTHER:searchPTHR12271PFAM:searchPF01909/searchPF03828SUPERFAMILY:searchSSF81301/searchSSF81631UniProt:searchO13833
JMol viewer RasMol script viewer  BR 402B  ..                                                                       ..                     ..        ..                                    *                     *                                                                                               ..BR ..                                                        
JMol viewer RasMol script viewer  MG 401B  ..                                                                       ..                     ..        ..                                    |                     |                                                                                               ..MG ..                                                        
sec str:  ....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.....eeeeehhhhhh.......eeeeee.....hhhhhhhhhhhh..eeeee.....eeeeee....eeeee.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh...hhhhh..hhhhhhhhhhhhhhhh.......hhhhh......ee..ee.....hhhhh.......hhhhhhhhhhhhhhhh......ee.........hhhhhh........ .......ee........hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhh..
sequence :  ..MSHKEFTKFCYEVYNEIKISDKEFKEKRAALDTLRLCLKRISPDAELVAFGSLESGLALKNSDMDLCVLMD..TIALQFYEELIAEGFEGKFLQ..IPIIKLTS..FQCAIGFNNRLAIHNTLLLSSYTKLDARLKPMVLLVKHWAKRKQINSPYFGTLSSYGYVLMVLYYLIHVIKPPVFPNLLLSPLKQEKIVDGFDVGFDDKLEDIPPSQNYSSLGSLLHGFFRFYAYKFEPREKVVTFRRPDGYLTKQEKGWTSAT... ..DRYILAIEDPFEISHNVGRTVSSSGLYRIRGEFMAASRLLNSRSYPIPYDSLFEEA
seq num:  ..39        49        59        69        79        89        99         ..116       126        ..140     ..157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307 ... ..322       332       342       352       362       372   
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  alphabetamotif ..              |  | |   |             ***** ||         | | |  |         ..         || |||      ..        ..                      |  | |              |||||  | | |   |                  ||| | |||       | |    |  |  | | ||   |         | | |  |  | || |||     | |    ..alphabetamotif..           |  |  |  |                 |  | |     *****  
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  nest ..              |  | |   |              |  | ||         *** |  |         ..         |  ***      ..        ..                      |  |                ****   *** |   |                   |  | |||       | |    |  |  | | ||   |         | | |  |  | || ***     ***    ..nest..           |  |  |  |                 |  | |      |  |  
search RasMol script viewer Motif-ligand binding stats  niche ..              **** |   |              *******             ****         ..         |    |      ..        ..                      ****                           |   |                   *******|       ***    ****  *****|   |         *** ****  ****                ..niche..           ****  ****                 ******      ****  
search RasMol script viewer Motif-ligand binding stats  schellmannloop ..                   |   |                 | |                           ..         ******      ..        ..                                                     |   |                      | | |                    | |  |   |                   | |                 ..schellmannloop..                                         | |            
search RasMol script viewer Motif-ligand binding stats  stmotif ..                   *****                 | |                           ..                     ..        ..                                                     *****                      *****                    | |  *****                   | |                 ..stmotif..                                         | |            
search RasMol script viewer Motif-ligand binding stats  stturn ..                                         ***                           ..                     ..        ..                                                                                ***                      ***                          ***                 ..stturn..                                         ***            

chain H : 5'-R(*AP*U)-3'
JMol viewer RasMol script viewer  BR 402B  .. *
sec str:  ....
sequence :  ..AU
seq num:  ..58

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