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)	5ooq (B)
Conformer 2 (PDB)	6ieh (B)
Window Length	7
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	658	2.56	119 - 618 620 - 620 731 - 742 871 - 1062
2	231	2.64	619 - 619 621 - 730 743 - 870

Sequence

`________________________________________________________________________________________________________________________` `5ooq(B) : MLADSFEQEASREVDASKGLTNSETLQVEQDGKVRLSHQVRHQVALPPNYDYTPIAp----------FTLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKNKQRVIYTSP` `:` `6ieh(B) : ***************************RVKVQSVETVEGCTHEVALPAEEDYLPLKPRVGKAAKEYPFILDAFQREAIQCVDNNQSVLVSAHTSAGKTVCAEYAIALALREKQRVIFTSP` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `5ooq(B) : IKALSNQKYRELLAEFGDVGLMTGDITINPDAGCLVMTTEILRSMLYRGSEVMREVAWVIFDEVHYMRDKERGVVWEETIILLPDKVRYVFLSATIPNAMEFAEWICKIHSQPCHIVYTN` `:` `6ieh(B) : IKALSNQKYREMYEEFQDVGLMTGDVTINPTASCLVMTTEILRSMLYRGSEVMREVAWVIFDEIHYMRDSERGVVWEETIILLPDNVHYVFLSATIPNARQFAEWICHLHKQPCHVIYTD` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `5ooq(B) : FRPTPLQHYLFPAHGDGIYLVVDEKSTFREENFQKAMASI-SkGD--IYKIVKMIWKKKYNPVIVFSFSKRDCEELALKMSKLDFNSDDEKEALTKIFNNAIALLPETDRELPQIKHILP` `:` `6ieh(B) : YRPTPLQHYIFPAGGDGLHLVVDENGDFREDNFNTAMQVLRDAGDsNVFKIVKMIMERNFQPVIIFSFSKKDCEAYALQMTKLDFNTDEEKKMVEEVFSNAIDCLSDEDKKLPQVEHVLP` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `5ooq(B) : LLRRGIGIHHSGLLPILKEVIEILFQEGFLKVLFATETF---lNMPAKTVVFTSVRKWDGQQFRWVSGGEYIQMSGRAGRRGLDDRGIVIMMIDEKMEPQVAKGMVKGQADRLDSAFHLG` `:` `6ieh(B) : LLKRGIGIHHGGLLPILKETIEILFSEGLIKALFATETFAMGINMPARTVLFTNARKFDGKDFRWISSGEYIQMSGRAGRRGMDDRGIVILMVDEKMSPTIGKQLLKGSADPLNSAFHLT` `________________________________________________________________________________________________________________________` `_____________________________618________________________________________________________________________________________` `5ooq(B) : YNMILNLMRVEGISPEFMLEHSFFQFQNVISVPVMEKKLAELKKDFDGIEVEDEENVKEYHEIEQAIKGYREDVRQVVTHPANALSFLQPGRLVEISVNGKDNYGWGAVVDFAKRIN-nP` `:` `6ieh(B) : YNMVLNLLRVEEINPEYMLEKSFYQFQHYRAIPGVVEKVKNSEEQYNKIVIPNEESVVIYYKIRQQLAKLGKEIEEYIHKPKYCLPFLQPGRLVKVKNEG-DDFGWGVVVNFSKKSNVKP` `_____________________________598________________________________________________________________________________________` `______________724_______________________________________________________________________________________________________` `5ooq(B) : SAVYTDHESYIVNVVVNTMYIDSPVNLLKPFNPTLPEGIRPAEEGEKSICAVIPITLDSIKSIGNLRLYMPKDIRASGQKETVGKSLREVNRRFPDGIPVLDPVKNMKIEDEDFLKLMKK` `:` `6ieh(B) : NSGELD-PLYVVEVLLRC----SKESL----KNSATEAAKPAKPDEKGEMQVVPVLVHLLSAISSVRLYIPKDLRPVDNRQSVLKSIQEVQKRFPDGIPLLDPIDDMGIQDQGLKKVIQK` `______________701_______________________________________________________________________________________________________` `________________________________________870_____________________________________________________________________________` `5ooq(B) : IDVLNTKLSSNPLTNSMRLEELYGKYSRKHDLHEDMKQLKRKISESQAVIQLDDLRRRKRVLRRLGFCTPNDIIELKGRVACEISSGDELLLTELIFNGNFNELKPEQAAALLSCFAFQE` `:` `6ieh(B) : VEAFEHRMYSHPLHNDPNLETVYTLCEKKAQIAIDIKSAKRELKKARTVLQMDELKCRKRVLRRLGFATSSDVIEMKGRVACEISSADELLLTEMMFNGLFNDLSAEQATALLSCFVFQE` `________________________________________839_____________________________________________________________________________` `________________________________________________________________________________________________________________________` `5ooq(B) : RCKEAPRLKPELAEPLKAMREIAAKIAKIMKDSKIEVVEKDYVESFRHELMEVVYEWCRGATFTQICKMTDVYEGSLIRMFKRLEELVKELVDVANTIGNSSLKEKMEAVLKLIHRDIVS` `:` `6ieh(B) : NSSEMPKLTEQLAGPLRQMQECAKRIAKVSAEAKLEIDEETYLSSFKPHLMDVVYTWATGATFAHICKMTDVFEGSIIRCMRRLEELLRQMCQAAKAIGNTELENKFAEGITKIKRDIVF` `________________________________________________________________________________________________________________________` `______` `5ooq(B) : AGSLYL` `:` `6ieh(B) : AASLYL` `______`

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)	20.5
Translation (A)	1.3
Closure (%)	44.9
Bending Residues ( green )	618 - 621 724 - 745 870 - 874
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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