DynDom - Protein Domain Motions

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)	6ieh (B)
Window Length	7
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	640	2.78	119 - 621 875 - 1062
2	236	3.31	622 - 868

Sequence

`________________________________________________________________________________________________________________________` `4qu4(A) : PVLADSFEQEASREVaSKGLTNSETLQVEQDGKVRLSHQVRHQVALPPNYDYTPIAEHKRVNEA-RTYPFTLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKNKQRVIYT` `:` `6ieh(B) : **************************RVKVQSVETVEGCTHEVALPAEEDYLPL--KPRVGKAAKEYPFILDAFQREAIQCVDNNQSVLVSAHTSAGKTVCAEYAIALALREKQRVIFT` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `4qu4(A) : SPIKALSNQKYRELLAEFGDVGLMTGDITINPDAGCLVMTTEILRSMLYRGSEVMREVAWVIFDEVHYMRDKERGVVWEETIILLPDKVRYVFLSATIPNAMEFAEWICKIHSQPCHIVY` `:` `6ieh(B) : SPIKALSNQKYREMYEEFQDVGLMTGDVTINPTASCLVMTTEILRSMLYRGSEVMREVAWVIFDEIHYMRDSERGVVWEETIILLPDNVHYVFLSATIPNARQFAEWICHLHKQPCHVIY` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `4qu4(A) : TNFRPTPLQHYLFPAHGDGIYLVVDEKSTFREENFQKAMASIaK-GD--IYKIVKMIWKKKYNPVIVFSFSKRDCEELALKMSKLDFNSDDEKEALTKIFNNAIALLPETDRELPQIKHI` `:` `6ieh(B) : TDYRPTPLQHYIFPAGGDGLHLVVDENGDFREDNFNTAMQVLRDAGDsNVFKIVKMIMERNFQPVIIFSFSKKDCEAYALQMTKLDFNTDEEKKMVEEVFSNAIDCLSDEDKKLPQVEHV` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `4qu4(A) : LPLLRRGIGIHHSGLLPILKEVIEILFQEGFLKVLFATETFSIGLNMPAKTVVFTSVRKWDGQQFRWVSGGEYIQMSGRAGRRGLDDRGIVIMMIDEKMEPQVAKGMVKGQADRLDSAFH` `:` `6ieh(B) : LPLLKRGIGIHHGGLLPILKETIEILFSEGLIKALFATETFAMGINMPARTVLFTNARKFDGKDFRWISSGEYIQMSGRAGRRGMDDRGIVILMVDEKMSPTIGKQLLKGSADPLNSAFH` `________________________________________________________________________________________________________________________` `__________________________________621___________________________________________________________________________________` `4qu4(A) : LGYNMILNLMRVEGISPEFMLEHSFFQFQNVISVPVMEKKLAELKKDFDGIEVEDEENVKEYHEIEQAIKGYREDVRQVVTHPANALSFLQPGRLVEISVNGKDNYGWGAVVDFAKRINK` `:` `6ieh(B) : LTYNMVLNLLRVEEINPEYMLEKSFYQFQHYRAIPGVVEKVKNSEEQYNKIVIPNEESVVIYYKIRQQLAKLGKEIEEYIHKPKYCLPFLQPGRLVKVKNEG-DDFGWGVVVNFSKKSNV` `__________________________________601___________________________________________________________________________________` `________________________________________________________________________________________________________________________` `4qu4(A) : RNPSAVYTDHESYIVNVVVNTMYIDSPVNLLKPFNPTLPEGIRPAEEGEKSICAVIPITLDSIKSIGNLRLYMPKDIRASGQKETVGKSLREVNRRFPDGIPVLDPVKNMKIEDEDFLKL` `:` `6ieh(B) : K-PNSGELD-PLYVVEVLLRC----SKESL----KNSATEAAKPAKPDEKGEMQVVPVLVHLLSAISSVRLYIPKDLRPVDNRQSVLKSIQEVQKRFPDGIPLLDPIDDMGIQDQGLKKV` `________________________________________________________________________________________________________________________` `_________________________________________868____________________________________________________________________________` `4qu4(A) : MKKIDVLNTKLSSNPLTNSMRLEELYGKYSRKHDLHEDMKQLKRKISEa--VIQLDDLRRRKRVLRRLGFCTPNDIIELKGRVACEISSGDELLLTELIFNGNFNELKPEQAAALLSC--` `:` `6ieh(B) : IQKVEAFEHRMYSHPLHNDPNLETVYTLCEKKAQIAIDIKSAKRELKKARTVLQMDELKCRKRVLRRLGFATSSDVIEMKGRVACEISSADELLLTEMMFNGLFNDLSAEQATALLSCFV` `_________________________________________837____________________________________________________________________________` `________________________________________________________________________________________________________________________` `4qu4(A) :` `--------------lAEPLKAMREIAAKIAKIMKDSKIEVVEKDYVESFRHELMEVVYEWCRG-tFTQICKMTDVYEGSLIRMFKRLEELVKELdVAtI---nSSLKEKMEAVLKLIHRD` `:` `6ieh(B) :` `FQENSSEMPKLTEQLAGPLRQMQECAKRIAKVSAEAKLEIDEETYLSSFKPHLMDVVYTWATGATFAHICKMTDVFEGSIIRCMRRLEELLRQMCQAAKAIGNTELENKFAEGITKIKRD` `________________________________________________________________________________________________________________________` `_________` `4qu4(A) : IVSAGSLY` `:` `6ieh(B) : IVFAASLYL` `_________`

Morph

This morph was created using the MorphIt_Pro protein morphing technique.
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Domain Pairs

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( red )	2
Rotation Angle (deg)	17.7
Translation (A)	3.4
Closure (%)	60.3
Bending Residues ( green )	621 - 622 868 - 875
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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