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

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	35	0.48	532 - 549 634 - 650
2	569	1.18	119 - 521 651 - 986
3	84	1.31	550 - 633

Sequence

`________________________________________________________________________________________________________________________` `2xgj(B) : HQVRHQVALPPNYDYTPIAEHKRVNEARTYPFTLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKNKQRVIYTSPIKALSNQKYRELLAEFGDVGLMTGDITINPDAGCLV` `:` `4u4c(A) : HQVRHQVALPPNYDYTPIAEHKRVNEARTYPFTLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKNKQRVIYTSPIKALSNQKYRELLAEFGDVGLMTGDITINPDAGCLV` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `2xgj(B) : MTTEILRSMLYRGSEVMREVAWVIFDEVHYMRDKERGVVWEETIILLPDKVRYVFLSATIPNAMEFAEWICKIHSQPCHIVYTNFRPTPLQHYLFPAHGDGIYLVVDEKSTFREENFQKA` `:` `4u4c(A) : MTTEILRSMLYRGSEVMREVAWVIFDEVHYMRDKERGVVWEETIILLPDKVRYVFLSATIPNAMEFAEWICKIHSQPCHIVYTNFRPTPLQHYLFPAHGDGIYLVVDEKSTFREENFQKA` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `2xgj(B) : MASIS--kGDIYKIVKMIWKKKYNPVIVFSFSKRDCEELALKMSKLDFNSDDEKEALTKIFNNAIALLPETDRELPQIKHILPLLRRGIGIHHSGLLPILKEVIEILFQEGFLKVLFATE` `:` `4u4c(A) : MASISNQkGDIYKIVKMIWKKKYNPVIVFSFSKRDCEELALKMSKLDFNSDDEKEALTKIFNNAIALLPETDRELPQIKHILPLLRRGIGIHHSGLLPILKEVIEILFQEGFLKVLFATE` `________________________________________________________________________________________________________________________` `_______________521________________________548___________________________________________________________________________` `2xgj(B) : TFSIG---pAKTVVFTSV----------vSGGEYIQMSGRAGRRGLDDRGIVIMMIDEKMEPQVAKGMVKGQADRLDSAFHLGYNMILNLMRVEGISPEFMLEHSFFQFQNVISVPVMEK` `:` `4u4c(A) : TFSIGLNMPAKTVVFTSVRKWDGQQFRWVSGGEYIQMSGRAGRRGLDDRGIVIMMIDEKMEPQVAKGMVKGQADRLDSAFHLGYNMILNLMRVEGISPEFMLEHSFFQFQNVISVPVMEK` `_______________521________________________548___________________________________________________________________________` `_______633______________650_____________________________________________________________________________________________` `2xgj(B) : KLAELKKDFDGIEVEDEENVKEYHEIEQAIKGYREDVRQVVTHPANAL------------------------------------------------------------------------` `:` `4u4c(A) : KLAELKKDFDGIEVEDEENVKEYHEIEQAIKGYREDVRQVVTHPANALSFLQPGRLVEISVNGKDNYGWGAVVDFAKRINvYTDHESYIVNVVVNTMYIDSPVNLLKPFNPTLPEGIRPA` `_______633______________650_____________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `2xgj(B) :` `------------------------------------------------------------pVKNMKIEDEDFLKLMKKIDVLNTKLSSNPLTNSMRLEELYGKYSRKHDLHEDMKQLKRK` `:` `4u4c(A) :` `EEGEKSICAVIPITLDSIKSIGNLRLYMPKDIRASGQKETVGKSLREVNRRFPDGIPVLDPVKNMKIEDEDFLKLMKKIDVLNTKLSSNPLTNSMRLEELYGKYSRKHDLHEDMKQLKRK` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `2xgj(B) : ISESQAVIQLDDLRRRKRVLRRLGFCTPNDIIELKGRVACEISSGDELLLTELIFNGNFNELKPEQAAALLSCFAFQERCKEAPRLKPELAEPLKAMREIAAKIAKIMKDSKIEVVEKDY` `:` `4u4c(A) : ISESQAVIQLDDLRRRKRVLRRLGFCTPNDIIELKGRVACEISSGDELLLTELIFNGNFNELKPEQAAALLSCFAFQERCKEAPRLKPELAEPLKAMREIAAKIAKIMKDSKIEVVEKDY` `________________________________________________________________________________________________________________________` `____________________________________________________________________________________` `2xgj(B) : VESFRHELMEVVYEWCRGATFTQICKMTDVYEGSLIRMFKRLEELVKELVDVANTIGNSSLKEKMEAVLKLIHRDIVSAGSLYL` `:` `4u4c(A) : VESFRHELMEVVYEWCRGATFTQICKMTDVYEGSLIRMFKRLEELVKELVDVANTIGNSSLKEKMEAVLKLIHRDIVSAGSLYL` `____________________________________________________________________________________`

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)	29.3
Translation (A)	-0.7
Closure (%)	55.0
Bending Residues ( green )	521 - 532 650 - 656
Bending Region Analysis

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( yellow )	3
Rotation Angle (deg)	22.4
Translation (A)	1.1
Closure (%)	98.5
Bending Residues ( green )	548 - 550 633 - 634
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification:

No Contacts

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

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

Movement classification:

No Contacts

PyMOL Script

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