D-Ribose-Binding Protein

(All numbering and residues are taken from first PDB file)

Run Details Domains Sequence Morph Domain Pairs Contact Graph

DynDom run details

  Property   Value
  Name D-Ribose-Binding Protein
  Conformer 1
(PDB)
1urp (A)
  Conformer 2
(PDB)
1urp (B)
  Window Length 5
  Minimum ratio 1.0
  Minimum domain size 20

Domains

Domain Size Backbone RMSD
(A)
Residues
1 102 0.04   3 - 102   235 - 236
2 132 0.03   103 - 234
3 29 0.04   237 - 265

Sequence


           ___________________________________________________________________________________________________102__________________ 
 1urp(A) : KDTIALVVSTLNNPFFVSLKDGAQKEADKLGYNLVVLDSQNNPAKELANVQDLTVRGTKILLINPTDSDAVGNAVKMANQANIPVITLDRQATKGEVVSHIASDNVLGGKIAGDYIAKKA 
         :                                                                                                                          
 1urp(B) : KDTIALVVSTLNNPFFVSLKDGAQKEADKLGYNLVVLDSQNNPAKELANVQDLTVRGTKILLINPTDSDAVGNAVKMANQANIPVITLDRQATKGEVVSHIASDNVLGGKIAGDYIAKKA 
           ___________________________________________________________________________________________________102__________________ 

           ______________________________________________________________________________________________________________233_______ 
 1urp(A) : GEGAKVIELQGIAGTSAARERGEGFQQAVAAHKFNVLASQPADFDRIKGLNVMQNLLTAHPDVQAVFAQNDEMALGALRALQTAGKSDVMVVGFDGTPDGEKAVNDGKLAATIAQLPDQI 
         :                                                                                                                          
 1urp(B) : GEGAKVIELQGIAGTSAARERGEGFQQAVAAHKFNVLASQPADFDRIKGLNVMQNLLTAHPDVQAVFAQNDEMALGALRALQTAGKSDVMVVGFDGTPDGEKAVNDGKLAATIAQLPDQI 
           ______________________________________________________________________________________________________________233_______ 

           _______________________________                                                                                          
 1urp(A) : GAKGVETADKVLKGEKVQAKYPVDLKLVVKQ                                                                                          
         :                                                                                                                          
 1urp(B) : GAKGVETADKVLKGEKVQAKYPVDLKLVVKQ                                                                                          
           _______________________________                                                                                          

Morph

This morph was created using the MorphIt_Pro protein morphing technique.
For more advanced options, right click on the model.


Show console


play backwards pause play forwards

Domain Pairs

Property Value
Fixed Domain
( blue )
1
Moving Domain
( red )
2
Rotation Angle
(deg)
1.3
Translation
(A)
0.1
Closure
(%)
10.4
Bending Residues
( green )
  102 - 105
  233 - 235
Bending Region Analysis
Property Value
Fixed Domain
( blue )
1
Moving Domain
( yellow )
3
Rotation Angle
(deg)
0.7
Translation
(A)
0.0
Closure
(%)
97.9
Bending Residues
( green )
  236 - 237
Bending Region Analysis

Dynamic Contact Graph

Conformer 1 Contact:
Residue 1 ———› Residue 2

Conformer 2 Contact:
Residue 2 ———› Residue 1

Movement classification:

No Contacts

Conformer 1 Contact:
Residue 1 ———› Residue 3

Conformer 2 Contact:
Residue 3 ———› Residue 1

Movement classification: Shear

PyMOL Script

Download and extract PyMOL PML script file Download