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

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	799	1.6	29 - 327 527 - 1144
2	148	1.07	328 - 526

Sequence

`________________________________________________________________________________________________________________________` `6vsb(C) : AYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFH-dNPVLPFNDGVYFASTnIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPF---fRVYSSANNCTFEYVSQP` `:` `6vsb(A) : AYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHfDNPVLPFNDGVYFASTnIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGeFRVYSSANNCTFEYVSQP` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `6vsb(C) : FLkNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALH-gAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNF` `:` `6vsb(A) : FLkNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRgAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNF` `________________________________________________________________________________________________________________________` `_____326________________________________________________________________________________________________________________` `6vsb(C) : RVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNS` `:` `6vsb(A) : RVQPTESIVR------lCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNS` `_____326________________________________________________________________________________________________________________` `_________________________________________________________525____________________________________________________________` `6vsb(C) : NNLDSyNYLYRnLKPFERDISTEnCYFPLQSYGFQ--vGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEIL` `:` `6vsb(A) : NNLDSyNYLYR----------------pLQSYGFQPTvGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEIL` `_________________________________________________________525____________________________________________________________` `________________________________________________________________________________________________________________________` `6vsb(C) : DITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEV-nVFQTRAGCLIGAEHVNNSYECDIPIGAGICAvASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDC` `:` `6vsb(A) : DITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVsNVFQTRAGCLIGAEHVNNSYECDIPIGAGICAvASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDC` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `6vsb(C) : TMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKrSFIEDLLFNKVTLqKFNGLTVLPPLLTDEMIAQYTSALLAGTITSG` `:` `6vsb(A) : TMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKrSFIEDLLFNKVTLqKFNGLTVLPPLLTDEMIAQYTSALLAGTITSG` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `6vsb(C) : WTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQ` `:` `6vsb(A) : WTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQ` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `6vsb(C) : TYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGN` `:` `6vsb(A) : TYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGN` `________________________________________________________________________________________________________________________` `_____________________` `6vsb(C) : CDVVIGIVNNTVYDPLQPELD` `:` `6vsb(A) : CDVVIGIVNNTVYDPLQPELD` `_____________________`

Morph

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Status: Initialising

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Domain Pairs

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( red )	2
Rotation Angle (deg)	60.0
Translation (A)	5.4
Closure (%)	35.3
Bending Residues ( green )	326 - 336 525 - 533
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification: Hinge

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