DynDom - Protein Domain Motions

Myosin Va

(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 Va
Conformer 1 (PDB)	1w8j (A)
Conformer 2 (PDB)	1w8j (D)
Window Length	9
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	622	1.05	9 - 463 479 - 693
2	82	0.77	464 - 478 694 - 760

Sequence

`________________________________________________________________________________________________________________________` `1w8j(A) : AASELYTKYARVWIPDPEEVWKSAELLKDYKPGDKVLQLRLdLEYCLDPKTKELPPLRNPDILVGENDLTALSYLHEPAVLHNLKVRFIDSKLIYTYCGIVLVAINPYEQLPIYGEDIIN` `:` `1w8j(D) : ***ELYTKYARVWIPDPEEVWKSAELLKDYKPGDKVLQLRLdLEYCLDPKTKELPPLRNPDILVGENDLTALSYLHEPAVLHNLKVRFIDSKLIYTYCGIVLVAINPYEQLPIYGEDIIN` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1w8j(A) : AYSGQNMGDMDPHIFAVAEEAYKQMARDERNQSIIVSGESGAGKTVSAKYAMRYFATVS---nVEEKVLASNPIMESIGNAKTTRNDNSSRFGKYIEIGFDKRYRIIGANMRTYLLEKSR` `:` `1w8j(D) : AYSGQNMGDMDPHIFAVAEEAYKQMARDERNQSIIVSGESGAGKTVSAKYAMRYFATVSGSAnVEEKVLASNPIMESIGNAKTTRNDNSSRFGKYIEIGFDKRYRIIGANMRTYLLEKSR` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1w8j(A) : VVFQAEEERNYHIFYQLCASAALPEFKTLRLGNANYFHYTKQGGSPVIDGIDDAKEMVNTRQACTLLGISDSYQMGIFRILAGILHLGNVEFASRDSDSCAIPPKHDPLTIFCDLMGVDY` `:` `1w8j(D) : VVFQAEEERNYHIFYQLCASAALPEFKTLRLGNANYFHYTKQGGSPVIDGIDDAKEMVNTRQACTLLGISDSYQMGIFRILAGILHLGNVEFASRDSDSCAIPPKHDPLTIFCDLMGVDY` `________________________________________________________________________________________________________________________` `__________________________________________________________________________________________461______________478__________` `1w8j(A) : EEMAHWLCHRKLATATETYIKPISKLHAINARDALAKHIYANLFNWIVDHVNKALHSTVKQHSFIGVLDIYGFETFEINSFEQFCINYANEKLQQQFNMHVFKLEQEEYMKEQIPWTLID` `:` `1w8j(D) : EEMAHWLCHRKLATATETYIKPISKLHAINARDALAKHIYANLFNWIVDHVNKALHSTVKQHSFIGVLDIYGFETFEINSFEQFCINYANEKLQQQFNMHVFKLEQEEYMKEQIP----d` `__________________________________________________________________________________________461______________478__________` `________________________________________________________________________________________________________________________` `1w8j(A) : FYDNQPCINLIEAKMGVLDLLDEECKMPKGSDDTWAQKLYNTHLNKCALFEKPRLSNKAFIIKHFADKVEYQCEGFLEKNKDTVYEEQIKVLKSSKKFKLLPELFQtSKEHKKTVGHQFR` `:` `1w8j(D) : FYDNQPCINLIEAKMGVLDLLDEECKMPKGSDDTWAQKLYNTHLNKCALFEKPRLSNKAFIIKHFADKVEYQCEGFLEKNKDTVYEEQIKVLKSSKKFKLLPELF-tSKEHKKTVGHQFR` `________________________________________________________________________________________________________________________` `_________________________________________________693____________________________________________________________________` `1w8j(A) : NSLHLLMETLNATTPHYVRCIKPNDFKFPFTFDEKRAVQQLRACGVLETIRISAAGFPSRWTYQEFFSRYRVLMKQKDVLSDRKQTCKNVLEKLILDKDKYQFGKTKIFFRAGQVAYLEK` `:` `1w8j(D) : NSLHLLMETLNATTPHYVRCIKPNDFKFPFTFDEKRAVQQLRACGVLETIRISAAGFPSRWTYQEFFSRYRVLMKQKDVLSDRKQTCKNVLEKLILDKDKYQFGKTKIFFRAGQVAYLEK` `_________________________________________________693____________________________________________________________________` `_____` `1w8j(A) : IRADK` `:` `1w8j(D) : IRADK` `_____`

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)	9.0
Translation (A)	0.3
Closure (%)	40.8
Bending Residues ( green )	461 - 464 478 - 492 693 - 696
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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