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)
4qu4 (A)
  Conformer 2
(PDB)
2xgj (B)
  Window Length 5
  Minimum ratio 1.0
  Minimum domain size 20

Domains

Domain Size Backbone RMSD
(A)
Residues
1 383 2.51   321 - 505   512 - 577   584 - 589   594 - 594   883 - 1066
2 363 2.23   119 - 320   506 - 508   578 - 583   590 - 593   595 - 882

Sequence


           ________________________________________________________________________________________________________________________ 
 4qu4(A) : PVLADSFEQEASREVaSKGLTNSETLQVEQDGKVRLSHQVRHQVALPPNYDYTPIAEHKRVNEARTYPFTLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKNKQRVIYTS 
         :                                                                                                                          
 2xgj(B) : *************************************HQVRHQVALPPNYDYTPIAEHKRVNEARTYPFTLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKNKQRVIYTS 
           ________________________________________________________________________________________________________________________ 

           ______________________________________________________________________________________________________________________32 
 4qu4(A) : PIKALSNQKYRELLAEFGDVGLMTGDITINPDAGCLVMTTEILRSMLYRGSEVMREVAWVIFDEVHYMRDKERGVVWEETIILLPDKVRYVFLSATIPNAMEFAEWICKIHSQPCHIVYT 
         :                                                                                                                          
 2xgj(B) : PIKALSNQKYRELLAEFGDVGLMTGDITINPDAGCLVMTTEILRSMLYRGSEVMREVAWVIFDEVHYMRDKERGVVWEETIILLPDKVRYVFLSATIPNAMEFAEWICKIHSQPCHIVYT 
           ______________________________________________________________________________________________________________________32 

           0_______________________________________________________________________________________________________________________ 
 4qu4(A) : NFRPTPLQHYLFPAHGDGIYLVVDEKSTFREENFQKAMASIaKGDIYKIVKMIWKKKYNPVIVFSFSKRDCEELALKMSKLDFNSDDEKEALTKIFNNAIALLPETDRELPQIKHILPLL 
         :                                                                                                                          
 2xgj(B) : NFRPTPLQHYLFPAHGDGIYLVVDEKSTFREENFQKAMASISkGDIYKIVKMIWKKKYNPVIVFSFSKRDCEELALKMSKLDFNSDDEKEALTKIFNNAIALLPETDRELPQIKHILPLL 
           0_______________________________________________________________________________________________________________________ 

           _________________________________504_508__________________________________________________________________577___583___58 
 4qu4(A) : RRGIGIHHSGLLPILKEVIEILFQEGFLKVLFATETFSIGLNMPAKTVVFTSVRKWDGQQFRWVSGGEYIQMSGRAGRRGLDDRGIVIMMIDEKMEPQVAKGMVKGQADRLDSAFHLGYN 
         :                                                                                                                          
 2xgj(B) : RRGIGIHHSGLLPILKEVIEILFQEGFLKVLFATETFSIG---pAKTVVFTSV----------vSGGEYIQMSGRAGRRGLDDRGIVIMMIDEKMEPQVAKGMVKGQADRLDSAFHLGYN 
           _________________________________504_508__________________________________________________________________577___583___58 

           9_593___________________________________________________________________________________________________________________ 
 4qu4(A) : MILNLMRVEGISPEFMLEHSFFQFQNVISVPVMEKKLAELKKDFDGIEVEDEENVKEYHEIEQAIKGYREDVRQVVTHPANALSFLQPGRLVEISVNGKDNYGWGAVVDFAKRINKRNPS 
         :                                                                                                                          
 2xgj(B) : MILNLMRVEGISPEFMLEHSFFQFQNVISVPVMEKKLAELKKDFDGIEVEDEENVKEYHEIEQAIKGYREDVRQVVTHPANAL------------------------------------- 
           9_593___________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 4qu4(A) : AVYTDHESYIVNVVVNTMYIDSPVNLLKPFNPTLPEGIRPAEEGEKSICAVIPITLDSIKSIGNLRLYMPKDIRASGQKETVGKSLREVNRRFPDGIPVLDPVKNMKIEDEDFLKLMKKI 
         :                                                                                                                          
 2xgj(B) : -----------------------------------------------------------------------------------------------------pVKNMKIEDEDFLKLMKKI 
           ________________________________________________________________________________________________________________________ 

           ___________________________________________________882__________________________________________________________________ 
 4qu4(A) : DVLNTKLSSNPLTNSMRLEELYGKYSRKHDLHEDMKQLKRKISE--aVIQLDDLRRRKRVLRRLGFCTPNDIIELKGRVACEISSGDELLLTELIFNGNFNELKPEQAAALLSC------ 
         :                                                                                                                          
 2xgj(B) : DVLNTKLSSNPLTNSMRLEELYGKYSRKHDLHEDMKQLKRKISESQAVIQLDDLRRRKRVLRRLGFCTPNDIIELKGRVACEISSGDELLLTELIFNGNFNELKPEQAAALLSCFAFQER 
           ___________________________________________________882__________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 4qu4(A) : ----------lAEPLKAMREIAAKIAKIMKDSKIEVVEKDYVESFRHELMEVVYEWCRG-tFTQICKMTDVYEGSLIRMFKRLEELVKEL-dVA-tI-nSSLKEKMEAVLKLIHRDIVSA 
         :                                                                                                                          
 2xgj(B) : CKEAPRLKPELAEPLKAMREIAAKIAKIMKDSKIEVVEKDYVESFRHELMEVVYEWCRGATFTQICKMTDVYEGSLIRMFKRLEELVKELVDVANTIGNSSLKEKMEAVLKLIHRDIVSA 
           ________________________________________________________________________________________________________________________ 

           _____                                                                                                                    
 4qu4(A) : GSLY*                                                                                                                    
         :                                                                                                                          
 2xgj(B) : GSLYL                                                                                                                    
           _____                                                                                                                    

Morph

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Status: Initialising

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Domain Pairs

Property Value
Fixed Domain
( blue )
1
Moving Domain
( red )
2
Rotation Angle
(deg)
18.1
Translation
(A)
0.3
Closure
(%)
83.5
Bending Residues
( green )
  320 - 321
  504 - 506
  508 - 512
  577 - 578
  583 - 584
  589 - 590
  593 - 595
  882 - 883
Bending Region Analysis

Dynamic Contact Graph

The dynamic contact graph is still being generated. Progress: Initialising

PyMOL Script

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