DynDom - Protein Domain Motions

Spike Glycoprotein

(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	Spike Glycoprotein
Conformer 1 (PDB)	6vyb (B)
Conformer 2 (PDB)	6vyb (C)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	783	1.8	29 - 332 528 - 1145
2	155	0.53	333 - 527

Sequence

`________________________________________________________________________________________________________________________` `6vyb(B) : AYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHnPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPF--nNCTFEYVSfKNLREFVF` `:` `6vyb(C) : AYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHnPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVnCTFEYVSfKNLREFVF` `________________________________________________________________________________________________________________________` `_________________________________________________________________________________________________________________330____` `6vyb(B) : KN---yFKIYSKHTPIN---dLPQGFSALEPLVDLPIGINITRFQTLLaAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITN` `:` `6vyb(C) : KNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLa-YYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITN` `_________________________________________________________________________________________________________________330____` `________________________________________________________________________________________________________________________` `6vyb(B) : LCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYR` `:` `6vyb(C) : LCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSK---nYNYLYR` `________________________________________________________________________________________________________________________` `__________________________________________526___________________________________________________________________________` `6vyb(B) : kPFER----pLQSYGFQPTNGVGYQPYRVVVLSF------aTVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPG` `:` `6vyb(C) : kPFERDISTpLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPG` `__________________________________________526___________________________________________________________________________` `________________________________________________________________________________________________________________________` `6vyb(B) : TNTSNEVAVLYQDVNCTEVnVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTsQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLL` `:` `6vyb(C) : TNTSNEVAVLYQDVNCTEVnVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQT-qSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLL` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `6vyb(B) : LQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKsKRSFIEDLLFNKVTkFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAM` `:` `6vyb(C) : LQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKsKRSFIEDLLFNKVT--nGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAM` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `6vyb(B) : QMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRA` `:` `6vyb(C) : QMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRA` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `6vyb(B) : SANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDP` `:` `6vyb(C) : SANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDP` `________________________________________________________________________________________________________________________` `_______` `6vyb(B) : LQPELDS` `:` `6vyb(C) : LQPELDS` `_______`

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)	64.1
Translation (A)	5.2
Closure (%)	45.2
Bending Residues ( green )	330 - 338 526 - 532
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification: Hinge

PyMOL Script

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