Atp-Dependent RNA Helicase Dob1

(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 Atp-Dependent RNA Helicase Dob1
  Conformer 1
(PDB)
5ooq (B)
  Conformer 2
(PDB)
2xgj (A)
  Window Length 5
  Minimum ratio 1.0
  Minimum domain size 20

Domains

Domain Size Backbone RMSD
(A)
Residues
1 516 1.54   92 - 115   325 - 522   530 - 539   545 - 546   548 - 577   584 - 601   675 - 676   683 - 691   723 - 737   742 - 758   760 - 762   773 - 774   782 - 808   880 - 1071
2 428 1.77   82 - 91   116 - 324   523 - 529   540 - 544   547 - 547   578 - 583   602 - 674   677 - 682   692 - 722   738 - 741   759 - 759   763 - 772   775 - 781   809 - 879

Sequence


           __________91_____________________115____________________________________________________________________________________ 
 5ooq(B) : MLADSFEQEASREVDASKGLTNSETLQVEQDGKVRLSHQVRHQVALPPNYDYTPIA-----------pFTLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKNKQRVIYTS 
         :                                                                                                                          
 2xgj(A) : MLADSFEQEASREVDASKGLTNSETLQVEQDGKVRLSHQVRHQVALPPNYDYTPIAEHKRVNEARTYPFTLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKNKQRVIYTS 
           __________91_____________________115____________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 5ooq(B) : PIKALSNQKYRELLAEFGDVGLMTGDITINPDAGCLVMTTEILRSMLYRGSEVMREVAWVIFDEVHYMRDKERGVVWEETIILLPDKVRYVFLSATIPNAMEFAEWICKIHSQPCHIVYT 
         :                                                                                                                          
 2xgj(A) : PIKALSNQKYRELLAEFGDVGLMTGDITINPDAGCLVMTTEILRSMLYRGSEVMREVAWVIFDEVHYMRDKERGVVWEETIILLPDKVRYVFLSATIPNAMEFAEWICKIHSQPCHIVYT 
           ________________________________________________________________________________________________________________________ 

           __324___________________________________________________________________________________________________________________ 
 5ooq(B) : NFRPTPLQHYLFPAHGDGIYLVVDEKSTFREENFQKAMASISkGDIYKIVKMIWKKKYNPVIVFSFSKRDCEELALKMSKLDFNSDDEKEALTKIFNNAIALLPETDRELPQIKHILPLL 
         :                                                                                                                          
 2xgj(A) : NFRPTPLQHYLFPAHGDGIYLVVDEKSTFREENFQKAMASIS-gDIYKIVKMIWKKKYNPVIVFSFSKRDCEELALKMSKLDFNSDDEKEALTKIFNNAIALLPETDRELPQIKHILPLL 
           __324___________________________________________________________________________________________________________________ 

           ___________________________________________________522______________539__544______________________________577___583_____ 
 5ooq(B) : RRGIGIHHSGLLPILKEVIEILFQEGFLKVLFATETF---lNMPAKTVVFTSVRKWDGQQFRWVSGGEYIQMSGRAGRRGLDDRGIVIMMIDEKMEPQVAKGMVKGQADRLDSAFHLGYN 
         :                                                                                                                          
 2xgj(A) : RRGIGIHHSGLLPILKEVIEILFQEGFLKVLFATETFSIGLNMPAKTVVFTSVRKWDGQQFRWVSGGEYIQMSGRAGRRGLDDRGIVIMMIDEKMEPQVAKGMVKGQADRLDSAFHLGYN 
           ___________________________________________________522______________539__544______________________________577___583_____ 

           __________601______________________________________________________________________674_____682______691_________________ 
 5ooq(B) : MILNLMRVEGISPEFMLEHSFFQFQNVISVPVMEKKLAELKKDFDGIEVEDEENVKEYHEIEQAIKGYREDVRQVVTHPANALSFLQPGRLVEISVNGKDNYGWGAVVDFAKRIN--nPS 
         :                                                                                                                          
 2xgj(A) : MILNLMRVEGISPEFMLEHSFFQFQNVISVPVMEKKLAELKKDFDGIEVEDEENVKEYHEIEQAIKGYREDVRQVVTHPANALSFLQPGRLVEISVNGKDNYGWGAVVDFAKRINKRNPS 
           __________601______________________________________________________________________674_____682______691_________________ 

           ___________722____________737_741______________758_762_______772______781________________________808____________________ 
 5ooq(B) : AVYTDHESYIVNVVVNTMYIDSPVNLLKPFNPTLPEGIRPAEEGEKSICAVIPITLDSIKSIGNLRLYMPKDIRASGQKETVGKSLREVNRRFPDGIPVLDPVKNMKIEDEDFLKLMKKI 
         :                                                                                                                          
 2xgj(A) : AVYTDHESYIVNVVVNTMYIDSPVNLLKPFNPTLPEGIRPAEEGEKSICAVIPITLDSIKSIGNLRLYMPKDIRASGQKETVGKSLREVNRRFPDGIPVLDPVKNMKIEDEDFLKLMKKI 
           ___________722____________737_741______________758_762_______772______781________________________808____________________ 

           ________________________________________________879_____________________________________________________________________ 
 5ooq(B) : DVLNTKLSSNPLTNSMRLEELYGKYSRKHDLHEDMKQLKRKISESQAVIQLDDLRRRKRVLRRLGFCTPNDIIELKGRVACEISSGDELLLTELIFNGNFNELKPEQAAALLSCFAFQER 
         :                                                                                                                          
 2xgj(A) : DVLNTKLSSNPLTNSMRLEELYGKYSRKHDLHEDMKQLKRKISESQAVIQLDDLRRRKRVLRRLGFCTPNDIIELKGRVACEISSGDELLLTELIFNGNFNELKPEQAAALLSCFAFQER 
           ________________________________________________879_____________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 5ooq(B) : CKEAPRLKPELAEPLKAMREIAAKIAKIMKDSKIEVVEKDYVESFRHELMEVVYEWCRGATFTQICKMTDVYEGSLIRMFKRLEELVKELVDVANTIGNSSLKEKMEAVLKLIHRDIVSA 
         :                                                                                                                          
 2xgj(A) : CKEAPRLKPELAEPLKAMREIAAKIAKIMKDSKIEVVEKDYVESFRHELMEVVYEWCRGATFTQICKMTDVYEGSLIRMFKRLEELVKELVDVANTIGNSSLKEKMEAVLKLIHRDIVSA 
           ________________________________________________________________________________________________________________________ 

           _____                                                                                                                    
 5ooq(B) : GSLYL                                                                                                                    
         :                                                                                                                          
 2xgj(A) : GSLYL                                                                                                                    
           _____                                                                                                                    

Morph

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Domain Pairs

Property Value
Fixed Domain
( blue )
1
Moving Domain
( red )
2
Rotation Angle
(deg)
7.2
Translation
(A)
0.6
Closure
(%)
75.7
Bending Residues
( green )
  91 - 92
  115 - 116
  324 - 325
  522 - 531
  539 - 540
  544 - 548
  577 - 578
  583 - 584
  601 - 602
  674 - 677
  682 - 683
  691 - 692
  722 - 723
  737 - 738
  741 - 742
  758 - 760
  762 - 763
  772 - 775
  781 - 782
  808 - 809
  879 - 880
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification: Shear

PyMOL Script

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