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 (A)
Conformer 2 (PDB)	6vsb (B)
Window Length	13
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	734	1.04	294 - 297 314 - 1140
2	202	1.68	33 - 293 298 - 313

Sequence

`________________________________________________________________________________________________________________________` `6vxx(A) : AYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHdNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGV--------nCTFE` `:` `6vsb(B) : AYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFH----nPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLsEFRVYSSANNCTFE` `________________________________________________________________________________________________________________________` `______________________________________________________________________________________________293_________________313___` `6vxx(A) : YVS---fKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHaAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTS` `:` `6vsb(B) : YVSQPFLkNLREFVFKNIDGYFKIYSKHTP-------pQGFSALEPLVDLPIGINITRFQTLLa---AYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTS` `______________________________________________________________________________________________293_________________313___` `________________________________________________________________________________________________________________________` `6vxx(A) : NFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAW` `:` `6vsb(B) : NFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAW` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `6vxx(A) : NSNNLDSKgNYNYLYR--kPFERDI-------yFPLQSYGFQPTNvGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVR` `:` `6vsb(B) : NSNNLDS---yNYLYRnLKPFERDISTEIYnCYFPLQSYGFQPT-vGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVR` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `6vxx(A) : DPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEV---nVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTsQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEI` `:` `6vsb(B) : DPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVtGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICAv--ASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEI` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `6vxx(A) : LPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVT--kFNGLTVLPPLLTDEMI` `:` `6vsb(B) : LPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDP---SKrSFIEDLLFNKVTLqKFNGLTVLPPLLTDEMI` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `6vxx(A) : AQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAE` `:` `6vsb(B) : AQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAE` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `6vxx(A) : VQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFY` `:` `6vsb(B) : VQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFY` `________________________________________________________________________________________________________________________` `_____________________________________` `6vxx(A) : EPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDS` `:` `6vsb(B) : EPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELD*` `_____________________________________`

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)	8.1
Translation (A)	0.1
Closure (%)	28.8
Bending Residues ( green )	293 - 298 313 - 314
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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