DynDom - Protein Domain Motions

Spike Glycoprotein,fibritin

(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,fibritin
Conformer 1 (PDB)	8h3e (C)
Conformer 2 (PDB)	7m6h (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	239	3.19	37 - 55 65 - 211 219 - 289 305 - 314 596 - 609 616 - 648 650 - 658 662 - 666 671 - 695
2	327	3.19	29 - 36 56 - 64 212 - 218 290 - 304 315 - 595 610 - 615 649 - 649
3	427	4.18	659 - 661 667 - 670 696 - 1141

Sequence

`________36_________________55_______64__________________________________________________________________________________` `8h3e(C) : AYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVtKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYsWMESE` `:` `7m6h(A) : AYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIH-----dNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGV--------` `________36_________________55_______64__________________________________________________________________________________` `____________________________________________________211____218_________________________________________________________2` `8h3e(C) :` `FRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLgAAAYYVGYLQPRTFLLKYNENGTITD` `:` `7m6h(A) :` `--------nCTFEYVS-------------fKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALH------aAYYVGYLQPRTFLLKYNENGTITD` `____________________________________________________211____218_________________________________________________________2` `89____________304_______314_____________________________________________________________________________________________` `8h3e(C) : AVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEV` `:` `7m6h(A) : AVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEV` `89____________304_______314_____________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `8h3e(C) : RQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGP` `:` `7m6h(A) : RQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGP` `________________________________________________________________________________________________________________________` `_________________________________________________________________595___________609_613____________________648_______658_` `8h3e(C) : KKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHAgSNVFQTRAGCLIGAEHVNNS` `:` `7m6h(A) : KKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEV--------nVFQTRAGCLIGAEHVNNS` `_________________________________________________________________595___________609_613____________________648_______658_` `____666______________695________________________________________________________________________________________________` `8h3e(C) : YECDIPIGAGICASYQ-sQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKT` `:` `7m6h(A) : YECDIPIGAGICASYQTsQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKT` `____666______________695________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `8h3e(C) : PPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLAlICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSA` `:` `7m6h(A) : PPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVT-------kFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSA` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `8h3e(C) : IGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLM` `:` `7m6h(A) : IGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLM` `________________________________________________________________________________________________________________________` `_________________________________________________________________________________________________` `8h3e(C) : SFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPE***` `:` `7m6h(A) : SFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDS` `_________________________________________________________________________________________________`

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)	20.4
Translation (A)	-1.0
Closure (%)	65.9
Bending Residues ( green )	36 - 37 55 - 56 64 - 65 211 - 212 218 - 219 289 - 290 304 - 305 314 - 315 595 - 596 609 - 610 613 - 641 648 - 650
Bending Region Analysis

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( yellow )	3
Rotation Angle (deg)	16.6
Translation (A)	1.7
Closure (%)	93.3
Bending Residues ( green )	658 - 659 661 - 662 666 - 667 669 - 671 695 - 696
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

PyMOL Script

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