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)
4u4c (A)
  Conformer 2
(PDB)
6ieg (A)
  Window Length 5
  Minimum ratio 1.0
  Minimum domain size 20

Domains

Domain Size Backbone RMSD
(A)
Residues
1 706 2.27   119 - 635   736 - 749   858 - 1071
2 152 2.6   639 - 735   750 - 857

Sequence


           ________________________________________________________________________________________________________________________ 
 4u4c(A) : **********HQVRHQVALPPNYDYTPIAEHKRVNEA-RTYPFTLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKNKQRVIYTSPIKALSNQKYRELLAEFGDVGLMTGD 
         :                                                                                                                          
 6ieg(A) : RVKVQSVETVEGCTHEVALPAEEDYLPL--KPRVGKAAKEYPFILDAFQREAIQCVDNNQSVLVSAHTSAGKTVCAEYAIALALREKQRVIFTSPIKALSNQKYREMY----dVGLMTGD 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 4u4c(A) : ITINPDAGCLVMTTEILRSMLYRGSEVMREVAWVIFDEVHYMRDKERGVVWEETIILLPDKVRYVFLSATIPNAMEFAEWICKIHSQPCHIVYTNFRPTPLQHYLFPAHGDGIYLVVDEK 
         :                                                                                                                          
 6ieg(A) : VTINPTASCLVMTTEILRSMLYRGSEVMREVAWVIFDEIHYMRDSERGVVWEETIILLPDNVHYVFLSATIPNARQFAEWICHLHKQPCHVIYTDYRPTPLQHYIFPAGGDGLHLVVDEN 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 4u4c(A) : STFREENFQKAMASISNQkGDIYKIVKMIWKKKYNPVIVFSFSKRDCEELALKMSKLDFNSDDEKEALTKIFNNAIALLPETDRELPQIKHILPLLRRGIGIHHSGLLPILKEVIEILFQ 
         :                                                                                                                          
 6ieg(A) : GDFREDNFNTAMQVLRD--sNVFKIVKMIMERNFQPVIIFSFSKKDCEAYALQMTKLDFNTDEEKKMVEEVFSNAIDCLSDEDKKLPQVEHVLPLLKRGIGIHHGGLLPILKETIEILFS 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 4u4c(A) : EGFLKVLFATETFSIGLNMPAKTVVFTSVRKWDGQQFRWVSGGEYIQMSGRAGRRGLDDRGIVIMMIDEKMEPQVAKGMVKGQADRLDSAFHLGYNMILNLMRVEGISPEFMLEHSFFQF 
         :                                                                                                                          
 6ieg(A) : EGLIKALFATETFAMGINMPARTVLFTNARKF----fRWISSGEYIQMSGRAGRRGMDDRGIVILMVDEKMSPTIGKQLLKGSADPLNSAFHLTYNMVLNLLRVEEINPEYMLEKSFYQF 
           ________________________________________________________________________________________________________________________ 

           ____________________635____________________________________________________________________________720__________________ 
 4u4c(A) : QNVISVPVMEKKLAELKKDFDGIEVEDEENVKEYHEIEQAIKGYREDVRQVVTHPANALSFLQPGRLVEISVNGKDNYGWGAVVDFAKRINvYTDHESYIVNVVVNTMYIDSPVNLLKPF 
         :                                                                                                                          
 6ieg(A) : QHYRAIPGVVEKVKNSEEQYNKI---nEESVVIYYKIRQQLAKLGKEIEEYIHKPKYCLPFLQPGRLVKVKNEG-DDFGWGVVVNFSKl---------YVVEV------------LLRCS 
           ____________________615____________________________________________________________________________697__________________ 

           _______748_______________________________________________________________________________830____________________________ 
 4u4c(A) : NPTLPEGIRPAEEGEKSICAVIPITLDSIKSIGNLRLYMPKDIRASGQKETVGKSLREVNRRFPDGIPVLDPVKNMKIEDEDFLKLMKKIDVLNTKLSSNPLTNSMRLEELYGKYSRKHD 
         :                                                                                                                          
 6ieg(A) : KESLtEAAKPAKPDEKGEMQVVPVLVHLLSAISSVRLYIPKDLRPVDNRQSVLKSIQEVQKRFPDGIPLLDPIDDMGIQDQGLKKVIQKVEA-------------------------kAQ 
           _______717_______________________________________________________________________________799____________________________ 

           ________________________________________________________________________________________________________________________ 
 4u4c(A) : LHEDMKQLKRKISESQAVIQLDDLRRRKRVLRRLGFCTPNDIIELKGRVACEISSGDELLLTELIFNGNFNELKPEQAAALLSCFAFQERCKEAPRLKPELAEPLKAMREIAAKIAKIMK 
         :                                                                                                                          
 6ieg(A) : IAIDIKSAKRELKKARTVLQMDELKCRKRVLRRLGFATSSDVIEMKGRVACEISSADELLLTEMMFNGLFNDLSAEQATALLSCFVFQENSSEMPKLTEQLAGPLRQMQECAKRIAKVSA 
           ________________________________________________________________________________________________________________________ 

           _______________________________________________________________________________________________                          
 4u4c(A) : DSKIEVVEKDYVESFRHELMEVVYEWCRGATFTQICKMTDVYEGSLIRMFKRLEELVKELVDVANTIGNSSLKEKMEAVLKLIHRDIVSAGSLYL                          
         :                                                                                                                          
 6ieg(A) : EAKLEIDEETYLSSFKPHLMDVVYTWATGATFAHICKMTDVFEGSIIRCMRRLEELLRQMCQAAKAIGNTELENKFAEGITKIKRDIVFAASLYL                          
           _______________________________________________________________________________________________                          

Morph

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Domain Pairs

Property Value
Fixed Domain
( blue )
1
Moving Domain
( red )
2
Rotation Angle
(deg)
36.0
Translation
(A)
2.7
Closure
(%)
73.4
Bending Residues
( green )
  635 - 640
  720 - 746
  748 - 754
  830 - 858
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification: Mixed

PyMOL Script

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