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

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	176	1.02	11 - 14 83 - 94 103 - 118 123 - 211 245 - 256 446 - 451 476 - 478 481 - 481 483 - 487 645 - 678
2	148	0.95	34 - 82 95 - 102 119 - 122 488 - 497 679 - 755
3	373	2.52	212 - 244 257 - 442 452 - 475 479 - 480 482 - 482 513 - 644

Sequence

`___________14__________________________________________________________________82__________94_____102_____________118_12` `2aka(A) : NPIHDRTSDYHKYLKVKQGDSDLFKLTVSDKRYIWYNPDPKERDSYECGEIVSETSDSFTFKTVDGQDRQVKKDDANQRNPIKFDGVEDMSELSYLNEPAVFHNLRVRYNQDLIYTYSGL` `:` `1fmw(A) : NPIHDRTSDYHKYLKVKQGDSDLFKLTVSDKRYIWYNPDPKERDSYECGEIVSETSDSFTFKTVDGQDRQVKKDDANQRNPIKFDGVEDMSELSYLNEPAVFHNLRVRYNQDLIYTYSGL` `___________14__________________________________________________________________82__________94_____102_____________118_12` `2_____________________________________________________________________________202_______________________________________` `2aka(A) : FLVAVNPFKRIPIYTQEMVDIFKGRRRNEVAPHIFAISDVAYRSMLDDRQNQSLLITGESGAGKTENTKKVIQYLASVAGRNQANGSGVLEQQILQANPILEAFGNAKTTRNNNSSRFGK` `:` `1fmw(A) : FLVAVNPFKRIPIYTQEMVDIFKGRRRNEVAPHIFAISDVAYRSMLDDRQNQSLLITGESGAGKTENTKKVIQYLASVAGR------gVLEQQILQANPILEAFGNAKTTRNNNSSRFGK` `2_____________________________________________________________________________202_______________________________________` `244_______254___________________________________________________________________________________________________________` `2aka(A) : FIEIQFNSAGFISGASIQSYLLEKSRVVFQSETERNYHIFYQLLAGATAEEKKALHLAGPESFNYLNQSGCVDIKGVSDSEEFKITRQAMDIVGFSQEEQMSIFKIIAGILHLGNIKFEK` `:` `1fmw(A) : FIEIQFNNAGFISGASIQSYLLEKSRVVFQSETERNYHIFYQLLAGATAEEKKALHLAGPESFNYLNQSGCVDIKGVSDSEEFKITRQAMDIVGFSQEEQMSIFKIIAGILHLGNIKFEK` `244_______254___________________________________________________________________________________________________________` `___________________________________________________________________________439_________451_____________________475______` `2aka(A) : GAGEGAVLKDKTALNAASTVFGVNPSVLEKALMEPRILAGRDLVAQHLNVEKSSSSRDALVKALYGRLFLWLVKKINNVLCQERKAYFIGVLDISGFEIFKVNSFEQLCINYTNEKLQQF` `:` `1fmw(A) : GAGEGAVLKDKTALNAASTVFGVNPSVLEKALMEPRILAGRDLVAQHLNVEKSSSSRDALVKALYGRLFLWLVKKINNVLCQERKAYFIGVLDISGFEIFKVNSFEQLCINYTNEKLQQF` `___________________________________________________________________________439_________451_____________________475______` `___487_______497________________________________________________________________________________________________________` `2aka(A) : FNHHMFKLEQEEYLKEKINWTFIDFGLDSQATIDLIDGRQPPGILALLDEQSVFPNATDNTLITKLHSHFSKKNAKYEEPRFSKTEFGVTHYAGQVMYEIQDWLEKNKDPLQQDLELCFK` `:` `1fmw(A) : FNHHMFKVEQEEYLKEKI---------dSQATIDLIDGRQPPGILALLDEQSVFPNATDNTLITKLHSHFSKKNAKYEEPRFSKTEFGVTHYAGQVMYEIQDWLEKNKDPLQQDLELCFK` `___487_______497________________________________________________________________________________________________________` `________________________________________644_______________________________678___________________________________________` `2aka(A) : DSSDNVVTKLFNDPNIASRAKKGANFITVAAQYKEQLASLMATLETTNPHFVRCIIPNNKQLPAKLEDKVVLDQLRCNGVLEGIRITRKGFPNRIIYADFVKRYYLLAPNVPRDAEDSQK` `:` `1fmw(A) : DSSDNVVTKLFNDPNIASRA-----fITVAAQYKEQLASLMATLETTNPHFVRCIIPNNKQLPAKLEDKVVLDQLRCNGVLEGIRITRKGFPNRIIYADFVKRYYLLAPNVPRDAEDSQK` `________________________________________644_______________________________678___________________________________________` `____________________________________________` `2aka(A) : ATDAVLKHLNIDPEQYRFGITKIFFRAGQLARIEEAREQRISEI` `:` `1fmw(A) : ATDAVLKHLNIDPEQYRFGITKIFFRAGQLARIEEARE******` `____________________________________________`

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	10.2	-0.5	89.5	14 - 34 82 - 84 94 - 95 102 - 103 118 - 119 122 - 123 487 - 489 678 - 680	Bending Region Analysis
1	3	17.2	2.5	94.2	202 - 212 244 - 245 254 - 257 439 - 447 451 - 452 475 - 483 644 - 645	Bending Region Analysis
3	2	20.2	3.1	81.2	497 - 513	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: Hinge

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

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

Movement classification: Hinge

PyMOL Script

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