triangle PDBeMotif: 4ndh  
  coner Sequences coner   coner 3D motifs coner   coner Ligand environment coner   coner Ligand bonds coner
   
coner
   Search  |  PDB header search  |  Upload PDB file  |  Molecule binding  |  Pair bonds  |  Motif binding  |  3D environment  |  Motif inclusion  
coner
AstexViewer TM
Download original PDB file
Download xml file
Download structure factors file
Classification dna binding protein/dna    | release date: Sat, Oct 26, 2013
Title human aprataxin (aptx) bound to dna, amp, and zn - product c
Authors M.J.SCHELLENBERG, P.S.TUMBALE, R.S.WILLIAMS
Method X-RAY DIFFRACTION (resolution: 1.85Å)
PDBe Citation   
Small molecules:    search ZN ZN binding statistics ZN   search AMP AMP binding statistics AMP
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:
GSHMGHWSQGLKISMQDPKMQVYKDEQVVVIKDKYPKARYHWLVLPWTSISSLKAVAREHLELLKHMHTVGEKVIVDFAG
SSKLRFRLGYHAIPSMSHVHLHVISQDFDSPCLKNKKHWNSFNTEYFLESQAVIEMVQEAGRVTVRDGMPELLKLPLRCH
ECQQLLPSIPQLKEHLRKHWTQ
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 : APRATAXIN
member of: GENE3D:searchG3DSA_2.60.200.20/searchG3DSA_3.30.428.10PANTHER:searchPTHR12486/searchPTHR12486_SF4PFAM:searchPF11969PROSITE PATTERNS:searchPS00028/searchPS00892, PROSITE PROFILES:searchPS51084, SMART:searchSM00355SUPERFAMILY:searchSSF54197UniProt:searchQ7Z2E3
JMol viewer RasMol script viewer  ZN 402A  ..                                                                                                                                                              *  *            *   * 
JMol viewer RasMol script viewer  AMP 401A  ..          *  *                  *** *   * *                                               *  ***   * *                                                        |  |            |   | 
sec str:  .......hhhhhhhhhh.....eeee...eeeee........eeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.........eeeee.........hhhhhhhhhh..eeehhhhhhhhhhhh......hhhhhh...ee......ee.hhhhhhhhhhhhh
sequence :  ..GSHMGHWSQGLKISMQDPKMQVYKDEQVVVIKDKYPKARYHWLVLPWTSISSLKAVAREHLELLKHMHTVGEKVIVDFAGSSKLRFRLGYHAIPSMSHVHLHVISQDFDSPCLKNKKHWNSFNTEYFLESQAVIEMVQEAGRVTVRDGMPELLKLPLRCHECQQLLPSIPQLKEHLRKHW
seq num:  ..161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       
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  ZINC_FINGER_C2H2_1 ..  |  |  |    |  || ||   | ||    | |          | |   ||| ||| ||                    | |  |      | | | |    | | || || |   ||   | ||            | |        || ||   ^**^************^***^ 
search RasMol script viewer Motif-ligand binding stats  HIT_1 ..  |  |  |    |  || ||   | ||    | |          | |   ||| ||| ||                    | |  ******************* | || || |   ||   | ||            | |        || ||      | |           |  | 
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  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 ..                                                   | |                           | |             | |         | |       ***** |                                                      
search RasMol script viewer Motif-ligand binding stats  stturn ..                                                   ***                           ***             | |         ***           ***                                                      
search RasMol script viewer Motif-ligand binding stats  Catalytic site ..                                                                                                 * *                                                                                

chain D : 5'-D(P*GP*TP*TP*CP*TP*AP*GP*AP*AP*C)-3'
JMol viewer RasMol script viewer  AMP 401A  ..          
sec str:  ............
sequence :  ..GTTCTAGAAC
seq num:  ..1         

chain E : 5'-D(P*GP*TP*TP*CP*TP*AP*GP*AP*AP*C)-3'
sec str:  ............
sequence :  ..GTTCTAGAAC
seq num:  ..1         

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 : APRATAXIN
member of: GENE3D:searchG3DSA_2.60.200.20/searchG3DSA_3.30.428.10PANTHER:searchPTHR12486/searchPTHR12486_SF4PFAM:searchPF11969PROSITE PATTERNS:searchPS00028/searchPS00892, PROSITE PROFILES:searchPS51084, SMART:searchSM00355SUPERFAMILY:searchSSF54197UniProt:searchQ7Z2E3
JMol viewer RasMol script viewer  ZN 402B  ..                                                                                                                                                            *  *            *   * 
JMol viewer RasMol script viewer  AMP 401B  ..        *  *                *****       *                                               *   **   * *                                                        |  |            |   | 
sec str:  ....hhhhhhhhhhhh....eeee...eeeee........eeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeee.........eeeee.........hhhhhhhhhh..eeehhhhhhhhhhhh......hhhhhh...ee......ee.hhhhhhhhhhhhh
sequence :  ..HMGHWSQGLKISMQDPKMQVYKDEQVVVIKDKYPKARYHWLVLPWTSISSLKAVAREHLELLKHMHTVGEKVIVDFAGSSKLRFRLGYHAIPSMSHVHLHVISQDFDSPCLKNKKHWNSFNTEYFLESQAVIEMVQEAGRVTVRDGMPELLKLPLRCHECQQLLPSIPQLKEHLRKHW
seq num:  ..163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333     
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  ZINC_FINGER_C2H2_1 ..   |  |    |  || ||   |  |    | |          | |   ||||||| ||                 |  | |  |          | |    | | || || | | |||  | ||            | |        || ||   ^**^************^***^ 
search RasMol script viewer Motif-ligand binding stats  HIT_1 ..   |  |    |  || ||   |  |    | |          | |   ||||||| ||                 |  | |  ******************* | || || | | |||  | ||            | |        || ||      | |                
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  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 ..                                                 *****                         | |             | |         | |    |  ||  | |                                                      
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 G : 5'-D(P*GP*TP*TP*CP*TP*AP*GP*AP*AP*C)-3'
JMol viewer RasMol script viewer  AMP 401B  ..*         
sec str:  ............
sequence :  ..GTTCTAGAAC
seq num:  ..1         

chain H : 5'-D(P*GP*TP*TP*CP*TP*AP*GP*AP*AP*C)-3'
sec str:  ............
sequence :  ..GTTCTAGAAC
seq num:  ..1         

   New search    4ndh:  Sequences  |  3D motifs  |  Ligand environment  |   Ligand bonds   |  SPICE view  |  PDB  |  XML  |  Structure factors