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Classification transcription/dna    | release date: Thu, Jul 17, 2003
Title ternary complex of the dna binding domains of the oct1 and sox2 transcription factors with a 19mer oligonucleotide from the hoxb1 regulatory element
Authors D.C.WILLIAMS, G.M.CLORE
Method SOLUTION NMR
PDBe Citation   
Ligand bond colours:   *  covalent   *  ionic   *  hydrogen   *  electrostatic   *  van-der-waals   *  plane-atom   *  plane-plane   *  undefined  - Click here to show 5Å bonds
Chain A sequence:
GSHMEEPSDLEELEQFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNLSFKNMAKLKPLLEKWLNDAEN
LSSDSSLSSPSALNSPGIEGLSERRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEK
RINPPSS
Chain B sequence:
GSHMPDRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPDYKYRPR
RKTKTLMK
Residue colours:  hydrophilic   hydrophobic   intermediate 
    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 : TRANSCRIPTION FACTOR OCT-1
member of: CATH:search1.10.10.60/search1.10.260.40GENE3D:searchG3DSA_1.10.10.60/searchG3DSA_1.10.260.40PANTHER:searchPTHR11636/searchPTHR11636_SF47PFAM:searchPF00046/searchPF00157PRINTS:searchOCTAMER/searchPOUDOMAINPROSITE PATTERNS:searchPS00027/searchPS00035/searchPS00465, PROSITE PROFILES:searchPS50071/searchPS51179, SMART:searchSM00352/searchSM00389SUPERFAMILY:searchSSF46689/searchSSF47413UniProt:searchP14859
sec str:  ......hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh...hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh...
sequence :  ..EEPSDLEELEQFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNLSFKNMAKLKPLLEKWLNDAE..SIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKRIN
seq num:  ..5         15        25        35        45        55        65        75   ..110       120       130       140       150       160 
search RasMol script viewer Motif-ligand binding stats  ASN_GLYCOSYLATION ..|  |||||||||  ||| ||||||||  | |||| | |||  |||||||||||^***|  ||  |  || |  | ..  ||| ||    |  |    || | | ||| |||  |  | |||||||||||  
search RasMol script viewer Motif-ligand binding stats  CAMP_PHOSPHO_SITE ..|  |||||||||  ||| ||||||||  | |||| | |||  |||||||||||| | |  ||  |  || |  | ..  ||| ||    |  |    || | | ||| |||  |  | |||||||||||  
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  HOMEOBOX_1 ..    ||||||||   || |||||||   | ||||   | |  | |||||||||| | |  ||  |  || |  | ..   || ||             |   | ************************|  
search RasMol script viewer Motif-ligand binding stats  POU_1 ..    ||||||||   || *************|||   | |  | |||||||||| | |  ||  |  || |  | ..   || ||             |   |  || |||  |  | |||||||||||  
search RasMol script viewer Motif-ligand binding stats  POU_2 ..    ||||||||   || |||||||   | ||||   | |  ************** |  ||  |  || |  | ..   || ||             |   |  || |||  |  | |||||||||||  
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  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  ststaple ..                                                                           ..                     *****                            

chain B : TRANSCRIPTION FACTOR SOX-2
member of: CATH:search1.10.30.10GENE3D:searchG3DSA_1.10.30.10PANTHER:searchPTHR10270/searchPTHR10270_SF47PFAM:searchPF00505/searchPF12336PROSITE PROFILES:searchPS50118, SMART:searchSM00398SUPERFAMILY:searchSSF47095UniProt:searchP48431
sec str:  .........hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..........
sequence :  ..DRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPDYKYRPRRK
seq num:  ..206       216       226       236       246       256       266       276    
search RasMol script viewer Motif-ligand binding stats  CAMP_PHOSPHO_SITE ..          || ||  | ||||||  | |   | ||||||||||||||| ||  |  |||||||||  | |  **^
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  alphabetamotif ..          || ||  *******|  | |   |  |||||||| || *****  ***********|  |       
search RasMol script viewer Motif-ligand binding stats  betaturn ..          *****  ********  | |   |  *******| *******   ********** |  |       
search RasMol script viewer Motif-ligand binding stats  niche ..                        **** |   |      ****                      ****       
search RasMol script viewer Motif-ligand binding stats  ststaple ..                             *****                                           

chain C : 5'-D(*TP*GP*TP*CP*TP*TP*TP*GP*TP*CP*AP*TP*GP*CP*TP*AP*AP*TP*G)-3';
sec str:  .....................
sequence :  ..TGTCTTTGTCATGCTAATG
seq num:  ..301       311      

chain D : 5'-D(*CP*AP*TP*TP*AP*GP*CP*AP*TP*GP*AP*CP*AP*AP*AP*GP*AP*CP*A)-3';
sec str:  .....................
sequence :  ..CATTAGCATGACAAAGACA
seq num:  ..320       330      

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