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

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	223	0.95	119 - 322 577 - 583 601 - 617 874 - 876
2	431	1.53	323 - 576 584 - 600 877 - 1068
3	50	1.03	618 - 634 841 - 873
4	54	0.82	639 - 662 811 - 840
5	142	0.58	663 - 810

Sequence

`________________________________________________________________________________________________________________________` `5ooq(A) : MLADSFEQEASREVDASKGLTNSETLQVEQDGKVRLSHQVRHQVALPPNYDYTPIAEHKRV--------tLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKNKQRVIYTS` `:` `4u4c(A) : ***********************************HQVRHQVALPPNYDYTPIAEHKRVNEARTYPFTLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKNKQRVIYTS` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `5ooq(A) : PIKALSNQKYRELLAEFGDVGLMTGDITINPDAGCLVMTTEILRSMLYRGSEVMREVAWVIFDEVHYMRDKERGVVWEETIILLPDKVRYVFLSATIPNAMEFAEWICKIHSQPCHIVYT` `:` `4u4c(A) : PIKALSNQKYRELLAEFGDVGLMTGDITINPDAGCLVMTTEILRSMLYRGSEVMREVAWVIFDEVHYMRDKERGVVWEETIILLPDKVRYVFLSATIPNAMEFAEWICKIHSQPCHIVYT` `________________________________________________________________________________________________________________________` `322_____________________________________________________________________________________________________________________` `5ooq(A) : NFRPTPLQHYLFPAHGDGIYLVVDEKSTFREENFQKAMASIS---gDIYKIVKMIWKKKYNPVIVFSFSKRDCEELALKMSKLDFNSDDEKEALTKIFNNAIALLPETDRELPQIKHILP` `:` `4u4c(A) : NFRPTPLQHYLFPAHGDGIYLVVDEKSTFREENFQKAMASISNQkGDIYKIVKMIWKKKYNPVIVFSFSKRDCEELALKMSKLDFNSDDEKEALTKIFNNAIALLPETDRELPQIKHILP` `322_____________________________________________________________________________________________________________________` `___________________________________________________________________________________________________________576____583___` `5ooq(A) : LLRRGIGIHHSGLLPILKEVIEILFQEGFLKVLFATETF--gLNMPAKTVVFTSVRKWDGQQFRWVSGGEYIQMSGRAGRRGLDDRGIVIMMIDEKMEPQVAKGMVKGQADRLDSAFHLG` `:` `4u4c(A) : LLRRGIGIHHSGLLPILKEVIEILFQEGFLKVLFATETFSIGLNMPAKTVVFTSVRKWDGQQFRWVSGGEYIQMSGRAGRRGLDDRGIVIMMIDEKMEPQVAKGMVKGQADRLDSAFHLG` `___________________________________________________________________________________________________________576____583___` `___________600_____________616_______________634_________________________662____________________________________________` `5ooq(A) : YNMILNLMRVEGISPEFMLEHSFFQFQNVISVPVMEKKLAELKKDFDGIEVEDEENVKEYHEIEQAIKGYREDVRQVVTHPANALSFLQPGRLVEISVNGKDNYGWGAVVDFAKRINKRN` `:` `4u4c(A) : YNMILNLMRVEGISPEFMLEHSFFQFQNVISVPVMEKKLAELKKDFDGIEVEDEENVKEYHEIEQAIKGYREDVRQVVTHPANALSFLQPGRLVEISVNGKDNYGWGAVVDFAKRIN---` `___________600_____________616_______________634_________________________662____________________________________________` `_____________________________________________________________________________________________________810________________` `5ooq(A) :` `PSAVYTDHESYIVNVVVNTMYIDSPVNLLKPFNPTLPEGIRPAEEGEKSICAVIPITLDSIKSIGNLRLYMPKDIRASGQKETVGKSLREVNRRFPDGIPVLDPVKNMKIEDEDFLKLMK` `:` `4u4c(A) :` `---vYTDHESYIVNVVVNTMYIDSPVNLLKPFNPTLPEGIRPAEEGEKSICAVIPITLDSIKSIGNLRLYMPKDIRASGQKETVGKSLREVNRRFPDGIPVLDPVKNMKIEDEDFLKLMK` `_____________________________________________________________________________________________________810________________` `__________839________________________________874________________________________________________________________________` `5ooq(A) : KIDVLNTKLSSNPLTNSMRLEELYGKYSRKHDLHEDMKQLKRKISESQAVIQLDDLRRRKRVLRRLGFCTPNDIIELKGRVACEISSGDELLLTELIFNGNFNELKPEQAAALLSCFAFQ` `:` `4u4c(A) : KIDVLNTKLSSNPLTNSMRLEELYGKYSRKHDLHEDMKQLKRKISESQAVIQLDDLRRRKRVLRRLGFCTPNDIIELKGRVACEISSGDELLLTELIFNGNFNELKPEQAAALLSCFAFQ` `__________839________________________________874________________________________________________________________________` `________________________________________________________________________________________________________________________` `5ooq(A) : ERCKEAPRLKPELAEPLKAMREIAAKIAKIMKDSKIEVVEKDYVESFRHELMEVVYEWCRGATFTQICKMTDVYEGSLIRMFKRLEELVKELVDVANTIGNSSLKEKMEAVLKLIHRDIV` `:` `4u4c(A) : ERCKEAPRLKPELAEPLKAMREIAAKIAKIMKDSKIEVVEKDYVESFRHELMEVVYEWCRGATFTQICKMTDVYEGSLIRMFKRLEELVKELVDVANTIGNSSLKEKMEAVLKLIHRDIV` `________________________________________________________________________________________________________________________` `_______` `5ooq(A) : SAGSL` `:` `4u4c(A) : SAGSLYL` `_______`

Morph

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Domain Pairs

Fixed Domain	Moving Domain	Rotation Angle	Translation (A)	Closure	Bending Residues
1	2	14.2	0.6	98.3	322 - 323 576 - 577 583 - 584 600 - 601 874 - 879	Bending Region Analysis
1	3	28.2	0.9	11.3	616 - 618 873 - 876	Bending Region Analysis
4	3	15.2	1.4	94.7	634 - 642 839 - 847	Bending Region Analysis
4	5	9.4	-0.4	99.1	662 - 663 810 - 811	Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification: Hinge

Conformer 1 Contact:
Residue 1 ———› Residue 3

Conformer 2 Contact:
Residue 3 ———› Residue 1

Movement classification:

No Contacts

Conformer 1 Contact:
Residue 4 ———› Residue 3

Conformer 2 Contact:
Residue 3 ———› Residue 4

Movement classification: Hinge

Conformer 1 Contact:
Residue 4 ———› Residue 5

Conformer 2 Contact:
Residue 5 ———› Residue 4

Movement classification:

No Contacts

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