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)	7jwy (A)
Conformer 2 (PDB)	6xm3 (A)
Window Length	7
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	71	0.89	323 - 330 521 - 522 528 - 588
2	747	0.77	30 - 313 595 - 1138
3	193	0.75	331 - 520 523 - 527

Sequence

`________________________________________________________________________________________________________________________` `7jwy(A) : AYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHdNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVeSEFRVYSSANNC` `:` `6xm3(A) : AYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHdNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGV-----vYSSANNC` `________________________________________________________________________________________________________________________` `_______________________________________________________________________________________________________________________3` `7jwy(A) : TFEYVSQfKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTaYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKG` `:` `6xm3(A) : TFEYVSQfKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTaYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKG` `_______________________________________________________________________________________________________________________3` `13______________330_____________________________________________________________________________________________________` `7jwy(A) : IYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTG` `:` `6xm3(A) : IYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTG` `13______________330_____________________________________________________________________________________________________` `________________________________________________________________________________516________527__________________________` `7jwy(A) : CVIAWNSNNLDSKgNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLT` `:` `6xm3(A) : CVIAWNSNNLDSKgNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLT` `________________________________________________________________________________516________527__________________________` `________________________________588_____________________________________________________________________________________` `7jwy(A) : ESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICAS` `:` `6xm3(A) : ESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICAS` `________________________________588_____________________________________________________________________________________` `________________________________________________________________________________________________________________________` `7jwy(A) : YQTsQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQI` `:` `6xm3(A) : YQTsQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQI` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `7jwy(A) : LPDPSKPSKRSFIEDLLFNKVTLiKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSA` `:` `6xm3(A) : LPDPSKPSKRSFIEDLLFNKVTL--------------dLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSA` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `7jwy(A) : IGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLM` `:` `6xm3(A) : IGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLM` `________________________________________________________________________________________________________________________` `_________________________________________________________________________________________________` `7jwy(A) : SFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDS` `:` `6xm3(A) : SFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDS` `_________________________________________________________________________________________________`

Morph

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Status: Initialising

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)	17.1
Translation (A)	0.5
Closure (%)	36.7
Bending Residues ( green )	313 - 324 588 - 596
Bending Region Analysis

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( yellow )	3
Rotation Angle (deg)	16.4
Translation (A)	0.5
Closure (%)	93.0
Bending Residues ( green )	330 - 334 516 - 523 527 - 531
Bending Region Analysis

Dynamic Contact Graph

The dynamic contact graph is still being generated. Progress: Initialising

PyMOL Script

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