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

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	265	1.06	29 - 316 595 - 615 641 - 658 662 - 662 671 - 692
2	250	0.8	317 - 594 616 - 620
3	435	0.33	659 - 661 663 - 670 693 - 1145

Sequence

`________________________________________________________________________________________________________________________` `6vyb(A) : AYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHpVLPFNDGVYFASTEKSNIIRGWIFGTTLDSK--sLLIVNNATNVVIKVCEFQFCNDPFLGV-cTFEYVSfKNLREF` `:` `6vyb(C) : AYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFH--nPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVnCTFEYVSfKNLREF` `________________________________________________________________________________________________________________________` `_____________________________________________________________________________________________________316________________` `6vyb(A) : VFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLaAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNI` `:` `6vyb(C) : VFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLa-YYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNI` `_____________________________________________________________________________________________________316________________` `________________________________________________________________________________________________________________________` `6vyb(A) : TNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLD--nYNYLYRL` `:` `6vyb(C) : TNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKnYNYLYR-` `________________________________________________________________________________________________________________________` `_____________________________________________________________________________________________________________________594` `6vyb(A) :` `FRKSNLKPFERDISTfPLQSYGFQPTN-vGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGG` `:` `6vyb(C) :` `------kPFERDIST-pLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGG` `_____________________________________________________________________________________________________________________594` `__________________615_619________________658__________________692_______________________________________________________` `6vyb(A) : VSVITPGTNTSNEVAVLYQDVNCTEVnVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTqSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDST` `:` `6vyb(C) : VSVITPGTNTSNEVAVLYQDVNCTEVnVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTqSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDST` `__________________615_619________________658__________________692_______________________________________________________` `________________________________________________________________________________________________________________________` `6vyb(A) : ECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKsKRSFIEDLLFNKVTfNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQ` `:` `6vyb(C) : ECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKsKRSFIEDLLFNKVT-nGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQ` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `6vyb(A) : IPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRA` `:` `6vyb(C) : IPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRA` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `6vyb(A) : AEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNN` `:` `6vyb(C) : AEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNN` `________________________________________________________________________________________________________________________` `____________` `6vyb(A) : TVYDPLQPELDS` `:` `6vyb(C) : TVYDPLQPELDS` `____________`

Morph

This morph was created using the MorphIt_Pro protein morphing technique.
For more advanced options, right click on the model.

play backwards

pause

play forwards

Domain Pairs

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( red )	2
Rotation Angle (deg)	10.2
Translation (A)	0.7
Closure (%)	84.8
Bending Residues ( green )	316 - 317 594 - 595 615 - 616 619 - 641
Bending Region Analysis

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( yellow )	3
Rotation Angle (deg)	7.8
Translation (A)	0.1
Closure (%)	32.2
Bending Residues ( green )	658 - 671 692 - 693
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification: Shear

Conformer 1 Contact:
Residue 1 ———› Residue 3

Conformer 2 Contact:
Residue 3 ———› Residue 1

Movement classification: Shear

PyMOL Script

Download and extract PyMOL PML script file

Download