DynDom - Protein Domain Motions

Cellodextrin Phosphorylase

(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	Cellodextrin Phosphorylase
Conformer 1 (PDB)	5nz7 (A)
Conformer 2 (PDB)	5nz8 (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	641	0.45	3 - 474 479 - 498 513 - 516 529 - 532 625 - 627 781 - 784 802 - 815 818 - 821 839 - 842 850 - 872 874 - 889 893 - 894 898 - 899 901 - 913 915 - 945 955 - 967 969 - 980
2	239	0.57	475 - 478 499 - 512 517 - 528 539 - 624 628 - 780 785 - 795 816 - 817 822 - 838 843 - 849 873 - 873 890 - 892 895 - 897 900 - 900 914 - 914 946 - 954 968 - 968 981 - 982

Sequence

`________________________________________________________________________________________________________________________` `5nz7(A) : MITKVTARNNKITPVELLNQKFGNKINLGNFADAVFTDAAFKNVAGIANLPMKAPVMQVLMENCIVSKYLKQFVPDRSVCFVEEGQKFYIVLEDGQKIEVPEDVNKALKATVSDVKHWAG` `:` `5nz8(A) : MITKVTARNNKITPVELLNQKFGNKINLGNFADAVFTDAAFKNVAGIANLPMKAPVMQVLMENCIVSKYLKQFVPDRSVCFVEEGQKFYIVLEDGQKIEVPEDVNKALKATVSDVKHWAG` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `5nz7(A) : YLTEDGEHVIDLLKPAPGPHFYVNLLIGNRLGFKRTLQTTPKSVVDRFGRGSFRSHAATQVLATRFDMRQEENGFPANRQFYLYEDGKQIFYSALIDDNIVEATCKHSCNRTVIKYKTAC` `:` `5nz8(A) : YLTEDGEHVIDLLKPAPGPHFYVNLLIGNRLGFKRTLQTTPKSVVDRFGRGSFRSHAATQVLATRFDMRQEENGFPANRQFYLYEDGKQIFYSALIDDNIVEATCKHSCNRTVIKYKTAC` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `5nz7(A) : NLEITRTIFLVPHKKGFPLATELQRIEIKNASDKARNLSITYTGMFGTGAVHAIFEDVTYTNVIMQSAALYNDKGEFIGITPDYYPEEFKQDTRFVTMIVRNGDEKSFPQSFCTDYNDFV` `:` `5nz8(A) : NLEITRTIFLVPHKKGFPLATELQRIEIKNASDKARNLSITYTGMFGTGAVHAIFEDVTYTNVIMQSAALYNDKGEFIGITPDYYPEEFKQDTRFVTMIVRNGDEKSFPQSFCTDYNDFV` `________________________________________________________________________________________________________________________` `_______________________________________________________________________________________________________________474_478__` `5nz7(A) : GTGTLEHPAGGCNLNNKLNRKGPGFFALGAPFTVEPGKTVIIDTFTGLSSSKDNENYSDAVMLRELDNLLRYFEKSESVEETLNEIINFHENYGKYFQFNTGNKLFDSGFNRNLAFQVLY` `:` `5nz8(A) : GTGTLEHPAGGCNLNNKLNRKGPGFFALGAPFTVEPGKTVIIDTFTGLSSSKDNENYSDAVMLRELDNLLRYFEKSESVEETLNEIINFHENYGKYFQFNTGNKLFDSGFNRNLAFQVLY` `_______________________________________________________________________________________________________________474_478__` `________491__________________512_516_________528________________________________________________________________________` `5nz7(A) : QTFMSRSFGQTQKGYREIGFREIQDLFASMYYFINIGYQDFVKELLFEWTANVYKMGYANHNFYWVGKQPGLYSDDSLWLLQAYYRYIIYTKDTSVLNEEVPVADGNNEKRAVRETLKAI` `:` `5nz8(A) : QTFMSRSFGQTQKGYREIGFREIQDLFASMYYFINIGYQDFVKELLFEWTAN------aNHNFYWVGKQPGLYSDDSLWLLQAYYRYIIYTKDTSVL-----------------------` `________491__________________512_516_________528________________________________________________________________________` `_____________________624________________________________________________________________________________________________` `5nz7(A) :` `IQYSACISVGDHGLPLLDLADWNDCLKIASNSIDGATKEKLYYEQLKKTNGKYGDRFMSDYSESVMNAFLLKLAIDHLAEIATLDNDTQLAQQMSELSKEVTDRIQKHAWKENFFARVLI` `:` `5nz8(A) :` `--------------------dWNDCLKI-----------------------------------sVMNAFLLKLAIDHLAEIATLD------qQMSELSKEVTDRIQKHAWKENFFARVLI` `_____________________624________________________________________________________________________________________________` `_________________________________________________________780_784_______794__________________815___821______________838_8` `5nz7(A) : NRYKDGSYTYLGAKGDKLSADPNIDGVYFLNSFAWSVLSDVATDEQIAIMVDVIKKHLLTPYGLRLVTPADLNKIANDTATGHYFFGDRENGAVFKHASMMAVAALIKAAKKVKDNELAK` `:` `5nz8(A) : NRY----yTYLGAKGDKLSADPNIDGVYFLNSFAWSVLSDVATDEQIAIMVDVIKKHLLTPYGLRLVTPADLNKI------gHYFFGDRENGAVFKHASMMAVAALIKAAKKVKDNELAK` `_________________________________________________________780_784_______794__________________815___821______________838_8` `42____849____________________872______________889_____897_____________913_____________________________945______954______` `5nz7(A) : EMARIAYFMIDLVLPYKNLENPFQVAGNPRICTQYINTDTGENIGPLLSGTATWLNLNLISLAGIEYTRDGISFNPILREEETQLNFTLKAPKCSYKFSITKPVGFARMESSEYELFVDG` `:` `5nz8(A) : EMARIAYFMIDLVLPYKNLENPFQVAGNPRICTQYINTDTGENIGPLLSGTATWLNLNLISLAGIEYTRDGISFNPILREEETQLNFTLKAPKCSYKFSITKPVGFARMESSEYELFVDG` `42____849____________________872______________889_____897_____________913_____________________________945______954______` `__965____________980____` `5nz7(A) : QKIDNTVIPMYTDEKEHIVTLKFK` `:` `5nz8(A) : QKIDNTVIPMYTDEKEHIVTLKFK` `__965____________980____`

Morph

This morph was created using the MorphIt_Pro protein morphing technique.
For more advanced options, right click on the model.

play backwards

pause

play forwards

Domain Pairs

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( red )	2
Rotation Angle (deg)	3.8
Translation (A)	0.0
Closure (%)	68.0
Bending Residues ( green )	474 - 475 478 - 479 491 - 499 512 - 513 516 - 517 528 - 529 531 - 539 624 - 625 627 - 628 780 - 781 784 - 785 794 - 803 815 - 818 821 - 822 838 - 839 842 - 843 849 - 850 872 - 874 889 - 890 892 - 895 897 - 901 913 - 915 945 - 946 954 - 955 965 - 969 980 - 981
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification: Shear

PyMOL Script

Download and extract PyMOL PML script file

Download