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)	6vxx (C)
Conformer 2 (PDB)	6vyb (C)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	706	0.83	313 - 597 602 - 604 612 - 612 616 - 642 645 - 648 658 - 660 664 - 666 668 - 669 674 - 691 693 - 1145
2	249	0.97	29 - 312 598 - 601 605 - 611 613 - 615 643 - 644 649 - 657 661 - 663 667 - 667 670 - 673 692 - 692

Sequence

`________________________________________________________________________________________________________________________` `6vxx(C) : AYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHdNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVnCTFEYVSfKNLR` `:` `6vyb(C) : AYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFH----nPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVnCTFEYVSfKNLR` `________________________________________________________________________________________________________________________` `______________________________________________________________________________________________________312_______________` `6vxx(C) : EFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHaAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIV` `:` `6vyb(C) : EFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLa----YYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIV` `______________________________________________________________________________________________________312_______________` `________________________________________________________________________________________________________________________` `6vxx(C) : RFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKgNY` `:` `6vyb(C) : RFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSK-nY` `________________________________________________________________________________________________________________________` `______________________________________________________________________________________________________________________59` `6vxx(C) : NYLYRkPFERDIyFPLQSYGFQPTN-vGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVS` `:` `6vyb(C) : NYLYRkPFERDISTpLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVS` `______________________________________________________________________________________________________________________59` `7_601_______611_615____642___648______657___663_______673___691_________________________________________________________` `6vxx(C) : VITPGTNTSNQVAVLYQDVNCTEVnVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTsQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTE` `:` `6vyb(C) : VITPGTNTSNEVAVLYQDVNCTEVnVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQT-qSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTE` `7_601_______611_615____642___648______657___663_______673___691_________________________________________________________` `________________________________________________________________________________________________________________________` `6vxx(C) : CSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTkFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAAL` `:` `6vyb(C) : CSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSK-sKRSFIEDLLFNKVT--nGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAAL` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `6vxx(C) : QIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIR` `:` `6vyb(C) : QIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIR` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `6vxx(C) : AAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVN` `:` `6vyb(C) : AAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVN` `________________________________________________________________________________________________________________________` `_____________` `6vxx(C) : NTVYDPLQPELDS` `:` `6vyb(C) : NTVYDPLQPELDS` `_____________`

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)	7.8
Translation (A)	-0.1
Closure (%)	10.1
Bending Residues ( green )	312 - 313 597 - 598 601 - 602 604 - 605 611 - 613 615 - 616 642 - 645 648 - 649 657 - 658 660 - 661 663 - 664 666 - 670 673 - 674 691 - 693
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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