DynDom - Protein Domain Motions

Excinuclease Abc, Subunit A.

(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	Excinuclease Abc, Subunit A.
Conformer 1 (PDB)	2vf7 (A)
Conformer 2 (PDB)	3pih (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	632	4.66	16 - 130 285 - 839
2	24	10.16	139 - 163
3	26	6.68	259 - 284

Sequence

`____________________________________________________________________________________________________________________129_` `2vf7(A) : PDGGFVQVRGARQHNLKDISVKVPRDALVVFTGVSGSGKSSLAFGTLYAEAQRRYLESVSPYARRLFNQAGVPDVDAIDGLPPAVALQQARGTPTARSSVGSVTTLSNLLRMLYSRAGD-` `:` `3pih(A) : **NEIVVKGARVHNLKNITVRIPKNRLVVITGVSGSGKSSLAMDTIYAEGQRRYLESLSTYkK--------PDVDEIEGLSPAIAIDQ-KTsHNPRSTVGTVTEIYDYLRVLYARIGKA` `____________________________________________________________________________________________________________________117_` `___________________________________________161__________________________________________________________________________` `2vf7(A) : YPP--GQGI-------VYAEGFSPNTPEGA-----CPECHGLGRVYTVTEDSMVPDPSLTIRE-------RAVAAWPQAWGGQNQRDILVTLGI--------DVDVPWRELPEETRHWIL` `:` `3pih(A) : HCPECGRPLEKKSIDEILQDLFN-SFKEGSRIYILAPlVVDRLILETRNEHRILDSLELAMREGKGFVEIRNVDTGESKIFSENLMCPVCGIGFPEITPKLFSFNSPYGACPNC--HGLG` `___________________________________________211__________________________________________________________________________` `_________________________________________________________________________284____________________________________________` `2vf7(A) : FTDE-QP-VVPVYPGLTPAETQRALKKKMEPSYMGTFSSARRHVLH-TFANT--------ESASMKKRVQ-GYMISEECPLCHGKRLRQEALNVTFAGLDITELSRLPLARVSELLRPYA` `:` `3pih(A) : FTFEVDPSLVaIIPYRWDRRLSRWVAREIEKRGVSPpEDVKEFILYGDfEGVVPKVQRWHRETeMKEWLEKNFIVQRTCSVCGGRRLNREALSVKINGLNIHEFTELSISEELEFLKNL-` `_________________________________________________________________________381____________________________________________` `________________________________________________________________________________________________________________________` `2vf7(A) :` `EEREPGHAERVKNRPEQAIALQRMAADLVKRLDVLLHLGLGYLGLDRSTPTLSPGELQRLRLATQLYSNLFGVVYVLDEPSAGLHPADTEALLSALENLKRGGNSLFVVEHDLDVIRRAD` `:` `3pih(A) :` `-----NLTER-----EREI-VGELLKEIEKRLEFLVDVGLEYLTLSRSATTLSGGESQRIRLATQIGSGLTGVIYVLDEPTIGLHPRDTERLIKTLKKLRDLGNTVIVVEHDEEVIRNAD` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `2vf7(A) : WLVDVGPEAGEKGGEILYSGPPEGLKHVPESQ-TGQYLFADRH-TEPHTPREPAGWLELNGVTRNNLDNLDVRFPLGVMTSVTGVSGSGKSTLVSQALVDALAAHFGQgSARLGG-DLAQ` `:` `3pih(A) : HIIDIGPGGGTNGGRVVFQGTVDELLKNPDSSLTGEYLSGKRKITVNKTRRLPYASLKIKGVRHNNLKNIDVEIPLGVFVCVTGVSGSGKSSLVMETLYPALMNLLHKTKLPAGEFDSIE` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `2vf7(A) :` `----ITRLVRVDQKPIGRTPRSNMATYTGLFDQVRKLFAATPLAKKRGYNAGRFSFNVKGGRCEHCQGEGWVMVELLFLPSVYAPCPVCHGTRYNAETLEVEYRGKNIADVLALTVDEAH` `:` `3pih(A) :` `GHENIDKMIAIDQSPIGRTPRSNPATYTKVFDEIRSLFAMTPAAKARGYNKSRFSFNLKGGRCEACQGQGYVKIEMLFLPDVYVECDVCKGKRYNRETLEITYKGKNISDILDMTVDEAL` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `2vf7(A) : DFFADESAIFRALDTLREVGLGYLRLGQPATELSGGEAQRIKLATELRRSGRGGTVYVLDEPTTGLHPADVERLQRQLVKLVDAGNTVIAVEHKMQVVAASDWVLDIGPGAGEDGGRLVA` `:` `3pih(A) : EFFKNIPSIKRTLQVLHDVGLGYVKLGQPATTLSGGEAQRIKLASELRKRDTGRTLYILDEPTVGLHFEDVRKLVEVLHRLVDRGNTVIVIEHNLDVIKNADHIIDLGPEGGKEGGYIVA` `________________________________________________________________________________________________________________________` `________________________` `2vf7(A) : QGTPAEVAQAAGSVTAPYLRAALR` `:` `3pih(A) : TGTPEEIAKNPHSYTGRFLKNVL` `________________________`

Morph

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Status: Initialising

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Domain Pairs

Fixed Domain	Moving Domain	Rotation Angle	Translation (A)	Closure	Bending Residues
1	2	156.3	2.6	22.7	129 - 139	Bending Region Analysis
1	3	100.4	-4.3	90.3	284 - 285	Bending Region Analysis
2	3	143.6	-14.6	91.2	161 - 259	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

Conformer 1 Contact:
Residue 2 ———› Residue 3

Conformer 2 Contact:
Residue 3 ———› Residue 2

Movement classification: Hinge

PyMOL Script

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