DynDom - Protein Domain Motions

Vinculin Isoform 1

(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	Vinculin Isoform 1
Conformer 1 (PDB)	1tr2 (A)
Conformer 2 (PDB)	1st6 (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	882	2.63	4 - 374 482 - 1059
2	106	1.69	375 - 481

Sequence

`________________________________________________________________________________________________________________________` `1tr2(A) : **PVFHTRTIESILEPVAQQISHLVI-hEEGEVDGKAIPDLTAPVAAVQAAVSNLVRVGKETVQTTEDQILKRD-pPAFIKVENACTKLVQAAQ-lQSDPYSVPARDYLIDGSRGILS` `:` `1st6(A) : VPRMPVFHTRTIESILEPVAQQISHLVIMHEEGEVDGKAIPDLTAPVSAVQAAVSNLVRVGKETVQTTEDQILKRDMPPAFIKVENACTKLVRAAQMLQADPYSVPARDYLIDGSRGILS` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1tr2(A) : GTSDLLLTFDEAEVRKIIRVCKGILEYLTVAEVVET-eDLVTYTKNLGPG-tK-aK-iDERQQELTHQEHRV-lVNS-nTVKELLPVLISA-kIFVTTKNSKNQGIEEALKNRNFTVEK-` `:` `1st6(A) : GTSDLLLTFDEAEVRKIIRVCKGILEYLTVAEVVETMEDLVTYTKNLGPGMTKMAKMIDERQQELTHQEHRVMLVNSMNTVKELLPVLISAMKIFVTTKNTKSQGIEEALKNRNFTVEKM` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1tr2(A) : sAEINEIIRVLQLTSWDEDAWASKDTEA-kRALASIDSKLNQAKGWLRDPSASPGDAGEQAIRQILDEAGKVGELCAGKERREILGTCK-lGQ-tDQVADLRARGQGSSPVA-qKAQQVS` `:` `1st6(A) : SAEINEIIRVLQLTSWDEDAWASKDTEAMKRALALIDSKMNQAKGWLRDPNAPPGDAGEQAIRQILDEAGKAGELCAGKERREILGTCKTLGQMTDQLADLRARGQGATPMAMQKAQQVS` `________________________________________________________________________________________________________________________` `______________374_______________________________________________________________________________________________________` `1tr2(A) : QGLDVLTAKVENAARKLEA-tNSKQSIAKKIDAAQNWLADPNGGPEGEEQIRGALAEARKIAELCDDPKERDDILRSLGEISALTSKLADLRRQGKGDSPEARALAKQVATALQNLQTKT` `:` `1st6(A) : QGLDLLTAKVENAARKLEAMTNSKQAIAKKIDAAQNWLADPNGGSEGEEHIRGIMSEARKVAELCEEPKERDDILRSLGEISALTAKLSDLRRHGKGDSPEARALAKQIATSLQNLQSKT` `______________374_______________________________________________________________________________________________________` `_481____________________________________________________________________________________________________________________` `1tr2(A) : NRAVANSRPAKAAVHLEGKIEQAQRWIDNPTVDDRGVGQAAIRGLVAEGHRLANV--gPYRQDLLAKCDRVDQLTAQLADLAARGEGESPQARALASQLQDSLKDLKAR-qEA-tQEVSD` `:` `1st6(A) : NRAVANTRPVKAAVHLEGKIEQAQRWIDNPTVDDRGVGQAAIRGLVAEGRRLANVMMGPYRQDLLAKCDRVDQLAAQLADLAARGEGESPQARAIAAQLQDSLKDLKARMQEAMTQEVSD` `_481____________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1tr2(A) : VFSDTTTPIKLLAVAATAPPDAPNREEVFDERAANFENHSGKLGATAEKAAAVGTANKSTVEGIQASVKTARELTPQVVSAARILLRNPGNQAAYEHFET-kNQWIDNVEK-tGLVDEAI` `:` `1st6(A) : VFSDTTTPIKLLAVAATAPSDTPNREEVFEERAANFENHAARLGATAEKAAAVGTANKTTVEGIQATVKSARELTPQVVSAARILLRNPGNQAAYEHFETMKNQWIDNVEKMTGLVDEAI` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1tr2(A) : DTKSLLDASEEAIKKDLDKCKVA-aNIQPQ-lVAGATSIARRANRILLVAKREVENSEDPKFREAVKAASDELSKTISPv--dAKAVAGNISDPGLQKSFLDSGYRILGAVAKVREAFQP` `:` `1st6(A) : DTKSLLDASEEAIKKDLDKCKVAMANMQPQMLVAGATSIARRANRILLVAKREVENSEDPKFREAVKAASDELSKTISPMVMDAKAVAGNISDPGLQKSFLDSGYRILGAVAKVREAFQP` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1tr2(A) : QEPDFPpP--------------EEKDEEFPEQKAGEVINQP---aARQLHDEARKWSSKGNDIIAAAKRa--LLaE-sRLVRGGSGTKRALIQCAKDIAKASDEVTRLAKEVAKQCTDKR` `:` `1st6(A) : QEPDFPPPPPDLEHLHLTpPPPEEKDEEFPEQKAGEAINQPMMMAARQLHDEARKWSSKGNDIIAAAKRMALLMAEMSRLVRGGSGNKRALIQCAKDIAKASDEVTRLAKEVAKQCTDKR` `________________________________________________________________________________________________________________________` `_________________________________________________________________________________________` `1tr2(A) : IRTNLLQVCERIPTISTQLKILSTVKAT-lGRTNISDEESEQATE-lVHNAQNL-qSVKETVREAEAASIKIRTDAGFTLRWVRK**` `:` `1st6(A) : IRTNLLQVCERIPTISTQLKILSTVKATMLGRTNISDEESEQATEMLVHNAQNLMQSVKETVREAEAASIKIRTDAGFTLRWVRKTPWY` `_________________________________________________________________________________________`

Morph

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Domain Pairs

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( red )	2
Rotation Angle (deg)	40.3
Translation (A)	0.0
Closure (%)	39.0
Bending Residues ( green )	374 - 375 481 - 482
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification: Hinge

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