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)	6zgf (A)
Conformer 2 (PDB)	7fg3 (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	800	7.78	29 - 316 534 - 576 582 - 1132
2	222	5.47	317 - 533 577 - 581

Sequence

`________________________________________________________________________________________________________________________` `6zgf(A) : QCVNLtQLPPAYTNSSTRGVYYPDKVFRSSVLHLTQDLFLPFFSNVTWFHrF-DNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYwM` `:` `7fg3(A) : ********AYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHdNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDP-------` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `6zgf(A) :` `ESEFRVYSSANNCTFEYVSQ------------fKNLREFVFKNIDGYFKIYSKHTPINLVRDLPPGFSALEPLVDLPIGINITRFQTLLALHRaAAYYVGYLQPRTFLLKYNENGTITDA` `:` `7fg3(A) :` `-----vYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLAtAGAAAYYVGYLQPRTFLLKYNENGTITDA` `________________________________________________________________________________________________________________________` `________________________315_____________________________________________________________________________________________` `6zgf(A) : VDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTDSIVRFPNITNLCPFGEVFNATTFASVYAWNRKRISNCVADYSVLYNSTSFSTFKCYGVSPTKLNDLCFTNVYADSFVITGDEVR` `:` `7fg3(A) : VDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVR` `________________________315_____________________________________________________________________________________________` `_______________________________________________________________________________________________________________________5` `6zgf(A) : QIAPGQTGKIADYNYKLPDDFTGCVIAWNSKHIDAKEGGNFNYLYRLFRKANLKPFERDISTEIYQAGSKPCNGQTGLNCYYPLYRYGFYPTDGVGHQPYRVVVLSFELLNAPATVCGPK` `:` `7fg3(A) : QIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPK` `_______________________________________________________________________________________________________________________5` `30_________________________________________574__________________________________________________________________________` `6zgf(A) : KSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAG` `:` `7fg3(A) : KSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAG` `30_________________________________________574__________________________________________________________________________` `________________________________________________________________________________________________________________________` `6zgf(A) : CLIGAEHVNNSYECDIPIGAGICASYQTQ-----------sQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALT` `:` `7fg3(A) : CLIGAEHVNNSYECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALT` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `6zgf(A) : GIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLkQYGDCLdLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAM` `:` `7fg3(A) : GIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAG------FIqKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAM` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `6zgf(A) : QMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRA` `:` `7fg3(A) : QMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRA` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `6zgf(A) : SANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGSCDVVIGIVNNTVYDP` `:` `7fg3(A) : SANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVY` `________________________________________________________________________________________________________________________` `____` `6zgf(A) : LQPE` `:` `7fg3(A) : ****` `____`

Morph

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)	63.0
Translation (A)	1.4
Closure (%)	40.3
Bending Residues ( green )	315 - 317 530 - 537 574 - 584
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification: Shear

Chart image not calculated - the graph is too big to count connection types.

PyMOL Script

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