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)	2xgj (A)
Window Length	7
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	506	1.77	83 - 90 122 - 171 174 - 318 508 - 509 579 - 582 590 - 592 594 - 883 889 - 894
2	427	2.36	91 - 121 172 - 173 319 - 507 510 - 578 583 - 589 593 - 593 884 - 888 895 - 1068

Sequence

`__________90____________________________121_______________________________________________171___________________________` `4qu4(A) : PVLADSFEQEASREV-aSKGLTNSETLQVEQDGKVRLSHQVRHQVALPPNYDYTPIAEHKRVNEARTYPFTLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKNKQRVIYT` `:` `2xgj(A) : MLADSFEQEASREVDASKGLTNSETLQVEQDGKVRLSHQVRHQVALPPNYDYTPIAEHKRVNEARTYPFTLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKNKQRVIYT` `__________90____________________________121_______________________________________________171___________________________` `_____________________________________________________________________________________________________________________318` `4qu4(A) : SPIKALSNQKYRELLAEFGDVGLMTGDITINPDAGCLVMTTEILRSMLYRGSEVMREVAWVIFDEVHYMRDKERGVVWEETIILLPDKVRYVFLSATIPNAMEFAEWICKIHSQPCHIVY` `:` `2xgj(A) : SPIKALSNQKYRELLAEFGDVGLMTGDITINPDAGCLVMTTEILRSMLYRGSEVMREVAWVIFDEVHYMRDKERGVVWEETIILLPDKVRYVFLSATIPNAMEFAEWICKIHSQPCHIVY` `_____________________________________________________________________________________________________________________318` `________________________________________________________________________________________________________________________` `4qu4(A) : TNFRPTPLQHYLFPAHGDGIYLVVDEKSTFREENFQKAMASIaKGDIYKIVKMIWKKKYNPVIVFSFSKRDCEELALKMSKLDFNSDDEKEALTKIFNNAIALLPETDRELPQIKHILPL` `:` `2xgj(A) : TNFRPTPLQHYLFPAHGDGIYLVVDEKSTFREENFQKAMASIS-gDIYKIVKMIWKKKYNPVIVFSFSKRDCEELALKMSKLDFNSDDEKEALTKIFNNAIALLPETDRELPQIKHILPL` `________________________________________________________________________________________________________________________` `____________________________________506_____________________________________________________________________578_582____5` `4qu4(A) : LRRGIGIHHSGLLPILKEVIEILFQEGFLKVLFATETFSIGLNMPAKTVVFTSVRKWDGQQFRWVSGGEYIQMSGRAGRRGLDDRGIVIMMIDEKMEPQVAKGMVKGQADRLDSAFHLGY` `:` `2xgj(A) : LRRGIGIHHSGLLPILKEVIEILFQEGFLKVLFATETFSIGLNMPAKTVVFTSVRKWDGQQFRWVSGGEYIQMSGRAGRRGLDDRGIVIMMIDEKMEPQVAKGMVKGQADRLDSAFHLGY` `____________________________________506_____________________________________________________________________578_582____5` `89______________________________________________________________________________________________________________________` `4qu4(A) : NMILNLMRVEGISPEFMLEHSFFQFQNVISVPVMEKKLAELKKDFDGIEVEDEENVKEYHEIEQAIKGYREDVRQVVTHPANALSFLQPGRLVEISVNGKDNYGWGAVVDFAKRINKRNP` `:` `2xgj(A) : NMILNLMRVEGISPEFMLEHSFFQFQNVISVPVMEKKLAELKKDFDGIEVEDEENVKEYHEIEQAIKGYREDVRQVVTHPANALSFLQPGRLVEISVNGKDNYGWGAVVDFAKRINKRNP` `89______________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `4qu4(A) : SAVYTDHESYIVNVVVNTMYIDSPVNLLKPFNPTLPEGIRPAEEGEKSICAVIPITLDSIKSIGNLRLYMPKDIRASGQKETVGKSLREVNRRFPDGIPVLDPVKNMKIEDEDFLKLMKK` `:` `2xgj(A) : SAVYTDHESYIVNVVVNTMYIDSPVNLLKPFNPTLPEGIRPAEEGEKSICAVIPITLDSIKSIGNLRLYMPKDIRASGQKETVGKSLREVNRRFPDGIPVLDPVKNMKIEDEDFLKLMKK` `________________________________________________________________________________________________________________________` `_____________________________________________________883__888___894_____________________________________________________` `4qu4(A) : IDVLNTKLSSNPLTNSMRLEELYGKYSRKHDLHEDMKQLKRKISE--aVIQLDDLRRRKRVLRRLGFCTPNDIIELKGRVACEISSGDELLLTELIFNGNFNELKPEQAAALLSC-----` `:` `2xgj(A) : IDVLNTKLSSNPLTNSMRLEELYGKYSRKHDLHEDMKQLKRKISESQAVIQLDDLRRRKRVLRRLGFCTPNDIIELKGRVACEISSGDELLLTELIFNGNFNELKPEQAAALLSCFAFQE` `_____________________________________________________883__888___894_____________________________________________________` `________________________________________________________________________________________________________________________` `4qu4(A) :` `-----------lAEPLKAMREIAAKIAKIMKDSKIEVVEKDYVESFRHELMEVVYEWCRG-tFTQICKMTDVYEGSLIRMFKRLEELVKEL-dVA-tI-nSSLKEKMEAVLKLIHRDIVS` `:` `2xgj(A) :` `RCKEAPRLKPELAEPLKAMREIAAKIAKIMKDSKIEVVEKDYVESFRHELMEVVYEWCRGATFTQICKMTDVYEGSLIRMFKRLEELVKELVDVANTIGNSSLKEKMEAVLKLIHRDIVS` `________________________________________________________________________________________________________________________` `______` `4qu4(A) : AGSLY` `:` `2xgj(A) : AGSLYL` `______`

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)	10.3
Translation (A)	0.8
Closure (%)	74.6
Bending Residues ( green )	90 - 91 121 - 122 171 - 178 318 - 319 506 - 510 578 - 579 582 - 583 589 - 590 592 - 594 883 - 884 888 - 889 894 - 895
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification: Shear

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