DynDom - Protein Domain Motions

Myosin

(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	Myosin
Conformer 1 (PDB)	1fmw (A)
Conformer 2 (PDB)	1mnd (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	197	0.73	10 - 192 449 - 450 653 - 674
2	267	0.69	199 - 240 244 - 448 591 - 619
3	140	1.2	241 - 243 452 - 590 633 - 647 675 - 679

Sequence

`________________________________________________________________________________________________________________________` `1fmw(A) : NPIHDRTSDYHKYLKVKQGDSDLFKLTVSDKRYIWYNPDPKERDSYECGEIVSETSDSFTFKTVDGQDRQVKKDDANQRNPIKFDGVEDMSELSYLNEPAVFHNLRVRYNQDLIYTYSGL` `:` `1mnd(A) : NPIHDRTSDYHKYLKVKQ--------tVSDKRYIWYNPDPDERDSYECGEIVSETSDSFTFKTV--qDRQVKKDDANQRNPIKFDGVEDMSELSYLNEPAVFHNLRVRYNQDLIYTYSGL` `________________________________________________________________________________________________________________________` `____________________________________________________________________192_______________________________________240_______` `1fmw(A) : FLVAVNPFKRIPIYTQEMVDIFKGRRRNEVAPHIFAISDVAYRSMLDDRQNQSLLITGESGAGKTENTKKVIQYLASVAGRgVLEQQILQANPILEAFGNAKTTRNNNSSRFGKFIEIQF` `:` `1mnd(A) : FLVAVNPFKRIPIYTQEMVDIFKGRRRNEVAPHIFAISDVAYRSMLDDRQNQSLLITGESGAGKTENTKKVIQYLASVAG--vLEQQILQANPILEAFGNAKTTRNNNSSRFGKFIEIQF` `____________________________________________________________________192_______________________________________240_______` `________________________________________________________________________________________________________________________` `1fmw(A) : NNAGFISGASIQSYLLEKSRVVFQSETERNYHIFYQLLAGATAEEKKALHLAGPESFNYLNQSGCVDIKGVSDSEEFKITRQAMDIVGFSQEEQMSIFKIIAGILHLGNIKFEKGAGEGA` `:` `1mnd(A) : NNAGFISGASIQSYLLEKSRVVFQSETERNYHIFYQLLAGATAEEKKALHLAGPESFNYLNQSGCVDIKGVSDEDEFKITRQAMDIVGFSQEEQMSIFKIIAGILHLGNIKFEKGAGEGA` `________________________________________________________________________________________________________________________` `______________________________________________________________________________448_______________________________________` `1fmw(A) : VLKDKTALNAASTVFGVNPSVLEKALMEPRILAGRDLVAQHLNVEKSSSSRDALVKALYGRLFLWLVKKINNVLCQERKAYFIGVLDISGFEIFKVNSFEQLCINYTNEKLQQFFNHHMF` `:` `1mnd(A) : VLKDKTALNAASTVFGVNPSVLEKALMEPRILAGRDLVAQHLNVEKSSSSRDALVKALYGRLFLWLVKKINNVLCS-rAAYFIGVLDISGFEIFKVNSFEQLCINYTNEKLQQFFNHHM-` `______________________________________________________________________________448_______________________________________` `___________________________________________________________________________________________590_______________________616` `1fmw(A) :` `KVEQEEYLKEKIdSQATIDLIDGRQPPGILALLDEQSVFPNATDNTLITKLHSHFSKKNAKYEEPRFSKTEFGVTHYAGQVMYEIQDWLEKNKDPLQQDLELCFKDSSDNVVTKLFNDPN` `:` `1mnd(A) :` `------------dSQATIDLIDGRQPPGILALLDEQSVFPNATDNTLITKLHSHFSKKNAKYEEPRFSKTEFGVTHYAGQVMYEIQDWLEKNKDPLQQDLELCFKDSSDNVVTKLFNDPN` `___________________________________________________________________________________________590_______________________616` `_______________________647________________________674___________________________________________________________________` `1fmw(A) : IASRAfITVAAQYKEQLASLMATLETTNPHFVRCIIPNNKQLPAKLEDKVVLDQLRCNGVLEGIRITRKGFPNRIIYADFVKRYYLLAPNVPRDAEDSQKATDAVLKHLNIDPEQYRFGI` `:` `1mnd(A) : IASR-fITVAAQYKEQLASLMATLETTNPHFVRCIIPNNKQLPAKLEDKVVLDQLRCNGVLE-iRITRK*************************************************` `_______________________647________________________674___________________________________________________________________` `__________________` `1fmw(A) : TKIFFRAGQLARIEEARE` `:` `1mnd(A) : ****************` `__________________`

Morph

This morph was created using the MorphIt_Pro protein morphing technique.
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Domain Pairs

Fixed Domain	Moving Domain	Rotation Angle	Translation (A)	Closure	Bending Residues
1	2	8.2	0.0	92.9	192 - 199 448 - 449	Bending Region Analysis
1	3	6.4	0.4	12.2	450 - 452 647 - 653 674 - 675	Bending Region Analysis
2	3	10.8	0.3	97.6	240 - 241 243 - 244 590 - 591 616 - 633	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: Hinge

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

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

Movement classification: Hinge

PyMOL Script

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