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

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	145	0.97	298 - 299 309 - 326 530 - 607 610 - 642 644 - 651 657 - 670 693 - 703
2	227	1.17	29 - 297 300 - 308 608 - 609 643 - 643 652 - 656 671 - 692
3	151	1.0	328 - 527
4	413	0.44	705 - 1144

Sequence

`________________________________________________________________________________________________________________________` `6vsb(B) : AYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFH--nPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLsEFRVYSSANNCTFEYV` `:` `6vsb(A) : AYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHfDNPVLPFNDGVYFAST---nIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGeFRVYSSANNCTFEYV` `________________________________________________________________________________________________________________________` `___________________________________________________________________________________________________297________308_______` `6vsb(B) : SQPFLkNLREFVFKNIDGYFKIYSKHTP-------pQGFSALEPLVDLPIGINITRFQTLLa------AYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQT` `:` `6vsb(A) : SQPFLkNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRgAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQT` `___________________________________________________________________________________________________297________308_______` `________326_____________________________________________________________________________________________________________` `6vsb(B) : SNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIA` `:` `6vsb(A) : SNFRVQPTESIVR------lCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIA` `________326_____________________________________________________________________________________________________________` `_______________________________________________________________526______________________________________________________` `6vsb(B) : WNSNNLDSyNYLYRnLKPFERDISTEIYnCYFPLQSYGFQPTvGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQ` `:` `6vsb(A) : WNSNNLDSyNYLYR------------------pLQSYGFQPTvGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQ` `_______________________________________________________________526______________________________________________________` `________________________607_______________642______651__656___________670_____692________703____________________________` `6vsb(B) : TLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVtGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICAvASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSM` `:` `6vsb(A) : TLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEV--sNVFQTRAGCLIGAEHVNNSYECDIPIGAGICAvASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSM` `________________________607_______________642______651__656___________670_____692________703____________________________` `________________________________________________________________________________________________________________________` `6vsb(B) : TKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKrSFIEDLLFNKVTLqKFNGLTVLPPLLTDEMIAQYTSALL` `:` `6vsb(A) : TKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKrSFIEDLLFNKVTLqKFNGLTVLPPLLTDEMIAQYTSALL` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `6vsb(B) : AGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLIT` `:` `6vsb(A) : AGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLIT` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `6vsb(B) : GRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTD` `:` `6vsb(A) : GRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTD` `________________________________________________________________________________________________________________________` `____________________________` `6vsb(B) : NTFVSGNCDVVIGIVNNTVYDPLQPELD` `:` `6vsb(A) : NTFVSGNCDVVIGIVNNTVYDPLQPELD` `____________________________`

Morph

Morph animation in progress.
Status: Initialising

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)	9.0
Translation (A)	-0.4
Closure (%)	20.2
Bending Residues ( green )	297 - 300 308 - 309 607 - 610 642 - 644 651 - 652 656 - 657 670 - 671 692 - 693
Bending Region Analysis

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( yellow )	3
Rotation Angle (deg)	61.5
Translation (A)	3.1
Closure (%)	50.9
Bending Residues ( green )	326 - 337 526 - 530
Bending Region Analysis

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( violet )	4
Rotation Angle (deg)	5.1
Translation (A)	0.8
Closure (%)	8.6
Bending Residues ( green )	703 - 705
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification: Hinge

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

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

Movement classification: Hinge

Conformer 1 Contact:
Residue 1 ———› Residue 4

Conformer 2 Contact:
Residue 4 ———› Residue 1

Movement classification:

No Contacts

PyMOL Script

Download and extract PyMOL PML script file

Download