RIBOKINASE
Ligand-induced domain movement details

Jmol view of liganded conformation 2

Domain Movement

domain 1 is binding domain(fixed in space)	domain 2 is binding domain(fixed in space)

Sequence

________13_______________________38_______________   1rka(A) : AGSLVVLGSINADHILNLQSFPTPGETVTGNHYQVAFGGKGANQAVAAGR           :                                                      1rkd    : AGSLVVLGSINADHILNLQSFPTPGETVTGNHYQVAFGGKGANQAVAAGR             ________13_______________________38_______________             ____________67____________________________97______   1rka(A) : SGANIAFIACTGDDSIGESVRQQLATDNIDITPVSVIKGESTGVALIFVN           :                                                      1rkd    : SGANIAFIACTGDDSIGESVRQQLATDNIDITPVSVIKGESTGVALIFVN             ____________67____________________________97______             ________114_______________________________________   1rka(A) : GEGENVIGIHAGANAALSPALVEAQRERIANASALLMQLESPLESVMAAA           :                                                      1rkd    : GEGENVIGIHAGANAALSPALVEAQRERIANASALLMQLESPLESVMAAA             ________114_______________________________________             __________________________________________________   1rka(A) : KIAHQNKTIVALNPAPARELPDELLALVDIITPNETEAEKLTGIRVENDE           :                                                      1rkd    : KIAHQNKTIVALNPAPARELPDELLALVDIITPNETEAEKLTGIRVENDE             __________________________________________________             __________________________________________________   1rka(A) : DAAKAAQVLHEKGIRTVLITLGSRGVWASVNGEGQRVPGFRVQAVDTIAA           :                                                      1rkd    : DAAKAAQVLHEKGIRTVLITLGSRGVWASVNGEGQRVPGFRVQAVDTIAA             __________________________________________________             __________________________________________________   1rka(A) : GDTFNGALITALLEEKPLPEAIRFAHAAAAIAVTRKGAQPSVPWREEIDA           :                                                      1rkd    : GDTFNGALITALLEEKPLPEAIRFAHAAAAIAVTRKGAQPSVPWREEIDA             __________________________________________________             ______                                               1rka(A) : FLDRQ*                                                       :                                                      1rkd    : FLDRQR                                                         ______

Details

Property   Value  Conformer 1 1rka(A)  Conformer 2 1rkd( )  Radius gyration for conformer 1 18.83 A  Radius gyration for conformer 2 18.44 A  EC Number 2.7.1.15   Click here to see the DynDom results or the famliy  Trigger ligands RIB311  Trigger ligands in which conformation Conformation  2  Conformaton with trigger ligands is compact Yes  Spanning ligands Yes  Residues in enzyme contacting ligands ALA98  ASN14  ASN46  ASP16  ASP255  GLU143  GLY41  GLY42  ILE100  ILE110  LYS43   Residues in extended bending regions contacting ligands ALA98  ASN14  ASP16  GLY41  GLY42  ILE100  LYS43   Residues in extended bending regions making H-bonds or salt-bridges with ligands ASN14  ASP16  GLY42  LYS43    Residues in extended bending regions with an H-bond between its main chain and ligands GLY42  LYS43  Click here to see the details of H-bonds between ligands and enzyme in PDF format generated by LIGPLOT