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)	7m6h (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	242	2.68	37 - 54 78 - 211 219 - 264 266 - 266 271 - 289 293 - 296 304 - 313 596 - 609 611 - 611 617 - 648 650 - 691
2	329	3.87	29 - 36 55 - 64 212 - 218 265 - 265 267 - 270 290 - 292 297 - 303 314 - 595 610 - 610 612 - 616 649 - 649
3	413	3.25	700 - 1138

Sequence

`__________________36________________54________64________________________________________________________________________` `6zgf(A) : QCVNLtQLPPAYTNSSTRGVYYPDKVFRSSVLHLTQDLFLPFFSNVTWFHrF-DNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYwM` `:` `7m6h(A) : ********AYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHdNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGV---` `__________________36________________54________64________________________________________________________________________` `___________________________________________211____218____________________________264___270________________289____296____` `6zgf(A) :` `ESEFRVYSSANNCTFEYVSQfKNLREFVFKNIDGYFKIYSKHTPINLVRDLPPGFSALEPLVDLPIGINITRFQTLLALHRaAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETK` `:` `7m6h(A) :` `-----------nCTFEYVS-fKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALH--aAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETK` `___________________________________________211____218____________________________264___270________________289____296____` `303_______313___________________________________________________________________________________________________________` `6zgf(A) : CTLKSFTVEKGIYQTSNFRVQPTDSIVRFPNITNLCPFGEVFNATTFASVYAWNRKRISNCVADYSVLYNSTSFSTFKCYGVSPTKLNDLCFTNVYADSFVITGDEVRQIAPGQTGKIAD` `:` `7m6h(A) : CTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIAD` `303_______313___________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `6zgf(A) : YNYKLPDDFTGCVIAWNSKHIDAKEGGNFNYLYRLFRKANLKPFERDISTEIYQAGSKPCNGQTGLNCYYPLYRYGFYPTDGVGHQPYRVVVLSFELLNAPATVCGPKKSTNLVKNKCVN` `:` `7m6h(A) : YNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVN` `________________________________________________________________________________________________________________________` `____________________________________________________595___________609____616_____________________________648____________` `6zgf(A) : FNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSY` `:` `7m6h(A) : FNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEV--------------------nVFQTRAGCLIGAEHVNNSY` `____________________________________________________595___________609____616_____________________________648____________` `_____________________691________________________________________________________________________________________________` `6zgf(A) : ECDIPIGAGICASYQTQsQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKT` `:` `7m6h(A) : ECDIPIGAGICASYQT-sQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKT` `_____________________695________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `6zgf(A) : PPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLkQYGDCLdLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLI` `:` `7m6h(A) : PPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVT--------------kFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLI` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `6zgf(A) : ANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFC` `:` `7m6h(A) : ANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFC` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________` `6zgf(A) : GKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGSCDVVIGIVNNTVYDPLQPE*` `:` `7m6h(A) : GKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDS` `________________________________________________________________________________________________________`

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)	19.6
Translation (A)	0.5
Closure (%)	63.9
Bending Residues ( green )	36 - 37 54 - 55 64 - 78 211 - 212 218 - 219 264 - 267 270 - 271 289 - 290 292 - 293 296 - 297 303 - 304 313 - 314 595 - 596 609 - 612 616 - 617 648 - 650
Bending Region Analysis

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( yellow )	3
Rotation Angle (deg)	15.5
Translation (A)	1.8
Closure (%)	89.0
Bending Residues ( green )	691 - 700
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:

No Contacts

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