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)
6ieg (A)
  Window Length 15
  Minimum ratio 1.0
  Minimum domain size 20

Domains

Domain Size Backbone RMSD
(A)
Residues
1 419 2.75   117 - 131   267 - 270   319 - 590   599 - 602   880 - 882   892 - 1065
2 413 4.59   132 - 266   271 - 318   591 - 598   603 - 879   883 - 891

Sequence


           _________________________________________________131____________________________________________________________________ 
 4qu4(A) : PVLADSFEQEASREVaSKGLTNSETLQVEQDGKVRLSHQVRHQVALPPNYDYTPIAEHKRVNEA-RTYPFTLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKNKQRVIYT 
         :                                                                                                                          
 6ieg(A) : ***************************RVKVQSVETVEGCTHEVALPAEEDYLPL--KPRVGKAAKEYPFILDAFQREAIQCVDNNQSVLVSAHTSAGKTVCAEYAIALALREKQRVIFT 
           _________________________________________________122____________________________________________________________________ 

           _________________________________________________________________266_270_____________________________________________318 
 4qu4(A) : SPIKALSNQKYRELLAEFGDVGLMTGDITINPDAGCLVMTTEILRSMLYRGSEVMREVAWVIFDEVHYMRDKERGVVWEETIILLPDKVRYVFLSATIPNAMEFAEWICKIHSQPCHIVY 
         :                                                                                                                          
 6ieg(A) : SPIKALSNQKYREMY----dVGLMTGDVTINPTASCLVMTTEILRSMLYRGSEVMREVAWVIFDEIHYMRDSERGVVWEETIILLPDNVHYVFLSATIPNARQFAEWICHLHKQPCHVIY 
           _________________________________________________________________256_260_____________________________________________308 

           ________________________________________________________________________________________________________________________ 
 4qu4(A) : TNFRPTPLQHYLFPAHGDGIYLVVDEKSTFREENFQKAMASIaKGDIYKIVKMIWKKKYNPVIVFSFSKRDCEELALKMSKLDFNSDDEKEALTKIFNNAIALLPETDRELPQIKHILPL 
         :                                                                                                                          
 6ieg(A) : TDYRPTPLQHYIFPAGGDGLHLVVDENGDFREDNFNTAMQVLRDsNVFKIVKMIMERNFQPVIIFSFSKKDCEAYALQMTKLDFNTDEEKKMVEEVFSNAIDCLSDEDKKLPQVEHVLPL 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 4qu4(A) : LRRGIGIHHSGLLPILKEVIEILFQEGFLKVLFATETFSIGLNMPAKTVVFTSVRKWDGQQFRWVSGGEYIQMSGRAGRRGLDDRGIVIMMIDEKMEPQVAKGMVKGQADRLDSAFHLGY 
         :                                                                                                                          
 6ieg(A) : LKRGIGIHHGGLLPILKETIEILFSEGLIKALFATETFAMGINMPARTVLFTNARKF----fRWISSGEYIQMSGRAGRRGMDDRGIVILMVDEKMSPTIGKQLLKGSADPLNSAFHLTY 
           ________________________________________________________________________________________________________________________ 

           590_____598_602_________________________________________________________________________________________________________ 
 4qu4(A) : NMILNLMRVEGISPEFMLEHSFFQFQNVISVPVMEKKLAELKKDFDGIEVEDEENVKEYHEIEQAIKGYREDVRQVVTHPANALSFLQPGRLVEISVNGKDNYGWGAVVDFAKRINKRNP 
         :                                                                                                                          
 6ieg(A) : NMVLNLLRVEEINPEYMLEKSFYQFQHYRAIPGVVEKVKNSEEQYNKI---nEESVVIYYKIRQQLAKLGKEIEEYIHKPKYCLPFLQPGRLVKVKNEG-DDFGWGVVVNFSKl------ 
           570_____578_582_________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 4qu4(A) : SAVYTDHESYIVNVVVNTMYIDSPVNLLKPFNPTLPEGIRPAEEGEKSICAVIPITLDSIKSIGNLRLYMPKDIRASGQKETVGKSLREVNRRFPDGIPVLDPVKNMKIEDEDFLKLMKK 
         :                                                                                                                          
 6ieg(A) : ---------YVVEV------------LLRCSKESLtEAAKPAKPDEKGEMQVVPVLVHLLSAISSVRLYIPKDLRPVDNRQSVLKSIQEVQKRFPDGIPLLDPIDDMGIQDQGLKKVIQK 
           ________________________________________________________________________________________________________________________ 

           _________________________________________________879_________891________________________________________________________ 
 4qu4(A) : IDVLNTKLSSNPLTNSMRLEELYGKYSRKHDLHEDMKQLKRKISEa--VIQLDDLRRRKRVLRRLGFCTPNDIIELKGRVACEISSGDELLLTELIFNGNFNELKPEQAAALLSC----- 
         :                                                                                                                          
 6ieg(A) : VEA-------------------------kAQIAIDIKSAKRELKKARTVLQMDELKCRKRVLRRLGFATSSDVIEMKGRVACEISSADELLLTEMMFNGLFNDLSAEQATALLSCFVFQE 
           _________________________________________________848_________860________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 4qu4(A) : -----------lAEPLKAMREIAAKIAKIMKDSKIEVVEKDYVESFRHELMEVVYEWCRG-tFTQICKMTDVYEGSLIRMFKRLEELVKELdVAtI---nSSLKEKMEAVLKLIHRDIVS 
         :                                                                                                                          
 6ieg(A) : NSSEMPKLTEQLAGPLRQMQECAKRIAKVSAEAKLEIDEETYLSSFKPHLMDVVYTWATGATFAHICKMTDVFEGSIIRCMRRLEELLRQMCQAAKAIGNTELENKFAEGITKIKRDIVF 
           ________________________________________________________________________________________________________________________ 

           ______                                                                                                                   
 4qu4(A) : AGSLY*                                                                                                                   
         :                                                                                                                          
 6ieg(A) : AASLYL                                                                                                                   
           ______                                                                                                                   

Morph

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Domain Pairs

Property Value
Fixed Domain
( blue )
1
Moving Domain
( red )
2
Rotation Angle
(deg)
17.8
Translation
(A)
1.0
Closure
(%)
37.3
Bending Residues
( green )
  131 - 132
  266 - 267
  270 - 271
  318 - 319
  590 - 591
  598 - 599
  602 - 603
  879 - 880
  882 - 883
  891 - 892
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification: Hinge

PyMOL Script

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