Atp-Dependent RNA Helicase Ddx58

(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 Ddx58
  Conformer 1
(PDB)
3tmi (A)
  Conformer 2
(PDB)
4a2w (A)
  Window Length 5
  Minimum ratio 1.0
  Minimum domain size 20

Domains

Domain Size Backbone RMSD
(A)
Residues
1 88 1.64   454 - 463   556 - 563   608 - 653   710 - 718   726 - 747
2 257 2.32   242 - 453   719 - 725   748 - 791
3 118 2.18   465 - 555   564 - 607

Sequence


           ________________________________________________________________________________________________________________________ 
 3tmi(A) : ************************************************************************************************************************ 
         :                                                                                                                          
 4a2w(A) : GTADEKRSLQCYRRYIERSLNPVYVLGNMTDWLPDELRERIRKEEERGVSGAAALFLDAVLQLEARGWFRGMLDAMLAAGYTGLAEAIENWDFSKLEKLELHRQLLKRIEATMLEVDPVA 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 3tmi(A) : ****************************************************************PFKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVF 
         :                                                                                                                          
 4a2w(A) : LIPYISTCLIDRECEEIQQISENRSKAAGITKLIECLCRSDKEHWPKSLQLALDTTGYYRASELWDkARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVF 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 3tmi(A) : FANQIPVYEQQKSVFSKYFERHGYRVTGISGATAENVPVEQIVENNDIIILTPQILVNNLKKGTIPSLSIFTLMIFDECHNTSKQHPYNMIMFNYLDQKLGGSSGPLPQVIGLTASVGVG 
         :                                                                                                                          
 4a2w(A) : LATKVPVYEQQKNVFKHHFERQGYSVQGISGEs-----VEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGNHPYNVLMTRYLEQKFNSAS-QLPQILGLTASVGVG 
           ________________________________________________________________________________________________________________________ 

           ___________________________________453_______463________________________________________________________________________ 
 3tmi(A) : DAKNTDEALDYICKLCASLDASVIATVKHNLEELEQVVYKPQKFFRKVESRISDKFKYIIAQLMRDTESLAKRICKDLENfGTQKYEQWIVTVQKAC----MVdKDEESRICKALFLYTS 
         :                                                                                                                          
 4a2w(A) : NAKNIEETIEHICSLCSYLDIQAISTVRENIQELQRFMNKPEIDVRLVKRRIHNPFAAIISNLMSETEALMRTI-----dFGTQNYEHWIVVTQRKCRLLQLEDKEEESRICRALFICTE 
           ___________________________________455_______465________________________________________________________________________ 

           _________555_____563_______________________________________605__________________________________________________________ 
 3tmi(A) : HLRKYNDALIISEHARMKDALDYLKDFFSNVRAAGFDEIEQDLTQRFEEKLQELESVSRDPSNENPKLEDLCFILQEEYHLNPETITILFVKTRALVDALKNWIEGNPKLSFLKPGILTG 
         :                                                                                                                          
 4a2w(A) : HLRKYNDALIISEDARIIDALSYLTEFFTNVKNGPYTELEQHLTAKFQEKEPELIALSKDETNENPKLEELVCILDDAYRYNPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVL-- 
           _________556_____564_______________________________________606__________________________________________________________ 

           __________________________________________________718__________________________747______________________________________ 
 3tmi(A) : RGKTNQNTGMTLPAQKCILDAFKAdHNILIATSVADEGIDIAQCNLVILYEYVGNVIKMIQTRGRGRARGSKCFLLTSNAGVIEKEQINMYKEKMMNDSILRLQTWDEAVFREKILHIQT 
         :                                                                                                                          
 4a2w(A) : ------------------------dNRLLIATSV------iVQCNLVVLYEYSGNVTKMIQV-------gSKCILVTSKTEVVENEKCNRYKEEMMNKAVEKIQKWDEETFAKKIHNLQM 
           __________________________________________________719__________________________748______________________________________ 

           ________________________________________________________________________________________________________________________ 
 3tmi(A) : HEKFIRDSQEKPKPVPDKENKKLLCRKCKALACYTADVRVIEECHYTVLGDAFKECFVSRPHPKPKQFSSFEKRAKIFCARQNCSHDWGIHVKYKTFEIPVIKIESFVVEDIATGVQTLY 
         :                                                                                                                          
 4a2w(A) : KERVLRDS**************************************************************************************************************** 
           ________________________________________________________________________________________________________________________ 

           __________________                                                                                                       
 3tmi(A) : SKWKDFHFEKIPFDPAEM                                                                                                       
         :                                                                                                                          
 4a2w(A) : ******************                                                                                                       
           __________________                                                                                                       

Morph

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Domain Pairs

Property Value
Fixed Domain
( blue )
1
Moving Domain
( red )
2
Rotation Angle
(deg)
42.8
Translation
(A)
2.0
Closure
(%)
49.7
Bending Residues
( green )
  453 - 454
  718 - 727
  747 - 749
Bending Region Analysis
Property Value
Fixed Domain
( blue )
1
Moving Domain
( yellow )
3
Rotation Angle
(deg)
23.4
Translation
(A)
-1.5
Closure
(%)
75.4
Bending Residues
( green )
  463 - 465
  555 - 556
  563 - 564
  605 - 608
Bending Region Analysis

Dynamic Contact Graph

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

PyMOL Script

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