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)
7dk3 (A)
  Conformer 2
(PDB)
7dk3 (C)
  Window Length 5
  Minimum ratio 1.0
  Minimum domain size 20

Domains

Domain Size Backbone RMSD
(A)
Residues
1 62 1.04   528 - 589
2 38 1.66   490 - 527
3 494 0.77   594 - 1145

Sequence


           ________________________________________________________________________________________________________________________ 
 7dk3(A) : QCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHkRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPF 
         :                                                                                                                          
 7dk3(C) : ************************************************************************************************************************ 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 7dk3(A) : LGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSsSGWTAGAAAYYV 
         :                                                                                                                          
 7dk3(C) : ************************************************************************************************************************ 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 7dk3(A) : GYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKL 
         :                                                                                                                          
 7dk3(C) : ************************************************************************************************************************ 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 7dk3(A) : NDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQP 
         :                                                                                                                          
 7dk3(C) : ****************************************************************************************************CYFPLQSYGFQPTNGVGYQP 
           ________________________________________________________________________________________________________________________ 

           ________________526____________________________________________________________589______________________________________ 
 7dk3(A) : YRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVnVFQTRA 
         :                                                                                                                          
 7dk3(C) : YRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVnVFQTRA 
           ________________526____________________________________________________________589______________________________________ 

           ________________________________________________________________________________________________________________________ 
 7dk3(A) : GCLIGAEHVNNSYECDIPIGAGICASYQTsQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQ 
         :                                                                                                                          
 7dk3(C) : GCLIGAEHVNNSYECDIPIGAGICASYQTsQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQ 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 7dk3(A) : EVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTkFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIAN 
         :                                                                                                                          
 7dk3(C) : EVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTkFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIAN 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 7dk3(A) : QFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGK 
         :                                                                                                                          
 7dk3(C) : QFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGK 
           ________________________________________________________________________________________________________________________ 

           ______________________________________________________________________________________________________                   
 7dk3(A) : GYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDS                   
         :                                                                                                                          
 7dk3(C) : GYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDS                   
           ______________________________________________________________________________________________________                   

Morph

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Domain Pairs

Property Value
Fixed Domain
( blue )
1
Moving Domain
( red )
2
Rotation Angle
(deg)
71.3
Translation
(A)
3.1
Closure
(%)
81.1
Bending Residues
( green )
  526 - 529
Bending Region Analysis
Property Value
Fixed Domain
( blue )
1
Moving Domain
( yellow )
3
Rotation Angle
(deg)
7.2
Translation
(A)
1.0
Closure
(%)
64.0
Bending Residues
( green )
  589 - 594
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:

No Contacts

PyMOL Script

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