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

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	669	2.2	119 - 617 872 - 1071
2	243	4.64	618 - 871

Sequence

`________________________________________________________________________________________________________________________` `4u4c(A) : **********HQVRHQVALPPNYDYTPIAEHKRVNEA-RTYPFTLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKNKQRVIYTSPIKALSNQKYRELLAEFGDVGLMTGD` `:` `6ieh(B) : RVKVQSVETVEGCTHEVALPAEEDYLPL--KPRVGKAAKEYPFILDAFQREAIQCVDNNQSVLVSAHTSAGKTVCAEYAIALALREKQRVIFTSPIKALSNQKYREMYEEFQDVGLMTGD` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `4u4c(A) : ITINPDAGCLVMTTEILRSMLYRGSEVMREVAWVIFDEVHYMRDKERGVVWEETIILLPDKVRYVFLSATIPNAMEFAEWICKIHSQPCHIVYTNFRPTPLQHYLFPAHGDGIYLVVDEK` `:` `6ieh(B) : VTINPTASCLVMTTEILRSMLYRGSEVMREVAWVIFDEIHYMRDSERGVVWEETIILLPDNVHYVFLSATIPNARQFAEWICHLHKQPCHVIYTDYRPTPLQHYIFPAGGDGLHLVVDEN` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `4u4c(A) : STFREENFQKAMASISNQkGD--IYKIVKMIWKKKYNPVIVFSFSKRDCEELALKMSKLDFNSDDEKEALTKIFNNAIALLPETDRELPQIKHILPLLRRGIGIHHSGLLPILKEVIEIL` `:` `6ieh(B) : GDFREDNFNTAM-QVLRDAGDsNVFKIVKMIMERNFQPVIIFSFSKKDCEAYALQMTKLDFNTDEEKKMVEEVFSNAIDCLSDEDKKLPQVEHVLPLLKRGIGIHHGGLLPILKETIEIL` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `4u4c(A) : FQEGFLKVLFATETFSIGLNMPAKTVVFTSVRKWDGQQFRWVSGGEYIQMSGRAGRRGLDDRGIVIMMIDEKMEPQVAKGMVKGQADRLDSAFHLGYNMILNLMRVEGISPEFMLEHSFF` `:` `6ieh(B) : FSEGLIKALFATETFAMGINMPARTVLFTNARKFDGKDFRWISSGEYIQMSGRAGRRGMDDRGIVILMVDEKMSPTIGKQLLKGSADPLNSAFHLTYNMVLNLLRVEEINPEYMLEKSFY` `________________________________________________________________________________________________________________________` `____617_________________________________________________________________________________________________________________` `4u4c(A) : QFQNVISVPVMEKKLAELKKDFDGIEVEDEENVKEYHEIEQAIKGYREDVRQVVTHPANALSFLQPGRLVEISVNGKDNYGWGAVVDFAKRINvYTDHESYIVNVVVNTMYIDSPVNLLK` `:` `6ieh(B) : QFQHYRAIPGVVEKVKNSEEQYNKIVIPNEESVVIYYKIRQQLAKLGKEIEEYIHKPKYCLPFLQPGRLVKVKNEG-DDFGWGVVVNFSKKSNVKPNSGELDPLYVVEVLLRCSKESL--` `____597_________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `4u4c(A) :` `PFNPTLPEGIRPAEEGEKSICAVIPITLDSIKSIGNLRLYMPKDIRASGQKETVGKSLREVNRRFPDGIPVLDPVKNMKIEDEDFLKLMKKIDVLNTKLSSNPLTNSMRLEELYGKYSRK` `:` `6ieh(B) :` `--KNSATEAAKPAKPDEKGEMQVVPVLVHLLSAISSVRLYIPKDLRPVDNRQSVLKSIQEVQKRFPDGIPLLDPIDDMGIQDQGLKKVIQKVEAFEHRMYSHPLHNDPNLETVYTLCEKK` `________________________________________________________________________________________________________________________` `____________871_________________________________________________________________________________________________________` `4u4c(A) : HDLHEDMKQLKRKISESQAVIQLDDLRRRKRVLRRLGFCTPNDIIELKGRVACEISSGDELLLTELIFNGNFNELKPEQAAALLSCFAFQERCKEAPRLKPELAEPLKAMREIAAKIAKI` `:` `6ieh(B) : AQIAIDIKSAKRELKKARTVLQMDELKCRKRVLRRLGFATSSDVIEMKGRVACEISSADELLLTEMMFNGLFNDLSAEQATALLSCFVFQENSSEMPKLTEQLAGPLRQMQECAKRIAKV` `____________840_________________________________________________________________________________________________________` `_________________________________________________________________________________________________` `4u4c(A) : MKDSKIEVVEKDYVESFRHELMEVVYEWCRGATFTQICKMTDVYEGSLIRMFKRLEELVKELVDVANTIGNSSLKEKMEAVLKLIHRDIVSAGSLYL` `:` `6ieh(B) : SAEAKLEIDEETYLSSFKPHLMDVVYTWATGATFAHICKMTDVFEGSIIRCMRRLEELLRQMCQAAKAIGNTELENKFAEGITKIKRDIVFAASLYL` `_________________________________________________________________________________________________`

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)	49.1
Translation (A)	-1.6
Closure (%)	40.8
Bending Residues ( green )	617 - 618 871 - 872
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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