DynDom - Protein Domain Motions

Genome Polyprotein

(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	Genome Polyprotein
Conformer 1 (PDB)	6kr2 (A)
Conformer 2 (PDB)	6kr3 (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	382	1.86	264 - 320 341 - 514 519 - 521 524 - 707
2	254	0.52	10 - 263
3	194	0.57	321 - 340 515 - 518 522 - 523 708 - 883

Sequence

`________________________________________________________________________________________________________________________` `6kr2(A) : TLGEKWKNRLNALGKSEFQIYKKSGIQEVDRTLAKEGIKRGETDHHAVSRGSAKLRWFVERNLVTPEGKVVDLGCGRGGWSYYCGGLKNVKEVKGLTKGGPGHEEPIPMSTYGWNLVRLQ` `:` `6kr3(A) : TLGEKWKNRLNALGKSEFQIYKKSGIQEVDRTLAKEGIKRGETDHHAVSRGSAKLRWFVERNLVTPEGKVVDLGCGRGGWSYYCGGLKNVKEVKGLTKGGPGHEEPIPMSTYGWNLVRLQ` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `6kr2(A) : SGVDVFFTPPEKCDTLLCDIGESSPNPTVEAGRTLRVLNLVENWLNNNTQFCIKVLNPYMPSVIEKMEALQRKYGGALVRNPLSRNSTHEMYWVSNASGNIVSSVNMISRMLINRFTMRH` `:` `6kr3(A) : SGVDVFFTPPEKCDTLLCDIGESSPNPTVEAGRTLRVLNLVENWLNNNTQFCIKVLNPYMPSVIEKMEALQRKYGGALVRNPLSRNSTHEMYWVSNASGNIVSSVNMISRMLINRFTMRH` `________________________________________________________________________________________________________________________` `____________262________________________________________________313________________________340___________________________` `6kr2(A) : KKATYEPDVDLGSGTRNIGIESETPNLDIIGKRIEKIKQEHETSWHYDQDHPYKTWAYHGSYETKQTGSASSMVNGVVRLLTKPWDIIPMVTQMAMTDTTPFGQQRVFKEKVDTRTQEPK` `:` `6kr3(A) : KKATYEPDVDLGSGTRNIGIESETPNLDIIGKRIEKIKQEHETSWHYDQDHPYKTWAYHGSYETKQT----sMVNGVVRLLTKPWDIIPMVTQMAMTDTTPFGQQRVFKEKVDTRTQEPK` `____________262________________________________________________313________________________340___________________________` `________________________________________________________________________________________________________________________` `6kr2(A) : EGTKKLMKITAEWLWKELGKKKTPRMCTREEFTRKVRSNwKSAREAVEDSGFWELVDKERNLHLEGKCETCVYNMMGKREKKLGEFGaKGSRAIWYMWLGARFLEFEALGFLNEDHWFSR` `:` `6kr3(A) : EGTKKLMKITAEWLWKELGKKKTPRMCTREEFTRKVRS-wKSAREAVEDSGFWELVDKERNLHLEGKCETCVYNMM--------------sRAIWYMWLGARFLEFEALGFLNEDHWFSR` `________________________________________________________________________________________________________________________` `_________512______521___________________________________________________________________________________________________` `6kr2(A) : ENSLSGVEGEGLHKLGYILRDVSKKEGGAMYADDTAGWDTRITLEDLKNEEMVTNHMEGEHKKLAEAIFKLTYQNKVVRVQRPTPRGTVMDIISRRDQRG----vTYGLNTFTNMEAQLI` `:` `6kr3(A) : ENSLSGVEGEGLHKLGYILRDVSKKEGGAMYADDTAGWDTRITLEDLKNEEMVTNHMEGEHKKLAEAIFKLTYQNKVVRVQRPTPRGTVMDIISRRDQRGSGQVVTYGLNTFTNMEAQLI` `_________512______521___________________________________________________________________________________________________` `____________________________________________________________________________________707_________________________________` `6kr2(A) : RQMEGEGVFKSIQHLTVTEEIAVKNWLVRVGRERLSRMAISGDDCVVKPLDDRFASALTALNDMGKVRKDIQQWEPSRGWNDWTQVPFCSHHFHELIMKDGRVLVVPCRNQDELIGRARI` `:` `6kr3(A) : RQMEGEGVFKSIQHLTVTEEIAVKNWLVRVGRERLSRMAISGDDCVVKPLDDRFASALTALNDMGKVRKDIQQWEPSRGWNDWTQVPFCSHHFHELIMKDGRVLVVPCRNQDELIGRARI` `____________________________________________________________________________________707_________________________________` `________________________________________________________________________________________________________________________` `6kr2(A) : SQ----sLRETACLGKSYAQMWSLMYFHRRDLRLAANAICSAVPSHWVPTSRTTWSIHATHEWMTTEDMLTVWNRVWIQENPWMEDKTPVESWEEIPYLGKREDQWCGSLIGLTSRATWA` `:` `6kr3(A) : SQGAGWSLRETACLGKSYAQMWSLMYFHRRDLRLAANAICSAVPSHWVPTSRTTW----tHEWMTTEDMLTVWNRVWIQENPWMEDKTPVESWEEIPYLGKREDQWCGSLIGLTSRATWA` `________________________________________________________________________________________________________________________` `_________________________` `6kr2(A) : KNIQTAINQVRSLIGNEEYTDYMPS` `:` `6kr3(A) : KNIQTAINQVRSLIGNEEYTDYMPS` `_________________________`

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)	81.8
Translation (A)	-3.8
Closure (%)	66.2
Bending Residues ( green )	262 - 270
Bending Region Analysis

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( yellow )	3
Rotation Angle (deg)	13.3
Translation (A)	-0.1
Closure (%)	1.9
Bending Residues ( green )	313 - 321 340 - 350 512 - 519 521 - 524 707 - 708
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

PyMOL Script

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