DynDom - Protein Domain Motions

Vitamin B12 Transporter Btub

(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	Vitamin B12 Transporter Btub
Conformer 1 (PDB)	1nqe (A)
Conformer 2 (PDB)	2gsk (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	509	1.49	14 - 394 398 - 399 413 - 442 457 - 592
2	30	0.81	395 - 397 400 - 412 443 - 456

Sequence

`________________________________________________________________________________________________________________________` `1nqe(A) : *DTLVVTANRFEQPRSTVLAPTTVVTRQDIDRWQSTSVNDVLRRLPGVDITQNGGSGQLSSIFIRGTNASHVLVLIDGVRLNLAGVSGSADLSQFPIALVQRVEYIRGPRSAVYGSDAIG` `:` `2gsk(A) : PDTLVVTANRFEQPRSTVLAPTTVVTRQDIDRWQSTSVNDVLRRLPGVDITQNGGSGQLSSIFIRGTNASHVLVLIDGVRLNLAGVSGSADLSQFPIALVQRVEYIRGPRSAVYGSDAIG` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1nqe(A) : GVVNIITTRDEPGTEISAGWGSNSYQNYDVSTQQQLGDKTRVTLLGDYAHTHG------------------gFLSKTLYGALEHNFTDAWSGFVRGYGYDNRTN------------dTRK` `:` `2gsk(A) : GVVNIITTRDEPGTEISAGWGSNSYQNYDVSTQQQLGDKTRVTLLGDYAHTHGYDVVAYGNTGTQAQTDNDGFLSKTLYGALEHNFTDAWSGFVRGYGYDNRTNYDAYYSPGSPLLDTRK` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1nqe(A) : LYSQSWDAGLRYNGELIKSQLITSYSHSKDYNY----------aTLDEMKQYTVQWANNVIVGHGSIGAGVDWQKQTTTPGTGYVEDGYDQRNTGIYLTGLQQVGDFTFEGAARSDDNSQ` `:` `2gsk(A) : LYSQSWDAGLRYNGELIKSQLITSYSHSKDYNYDPHYGRYDSSATLDEMKQYTVQWANNVIVGHGSIGAGVDWQKQTTTPGTGYVEDGYDQRNTGIYLTGLQQVGDFTFEGAARSDDNSQ` `________________________________________________________________________________________________________________________` `___________________________394_______________412___________________________442__________455_____________________________` `1nqe(A) : FGRHGTWQTSAGWEFIEGYRFIASYGTSYKAPNLGQLYGFYGNPNLDPEKSKQWEGAFEGLTAGVNWRISGYRNDVSDLIDYDDHTLKYYNEGKARIKGVEATANFDTGPLTHTVSYDYV` `:` `2gsk(A) : FGRHGTWQTSAGWEFIEGYRFIASYGTSYKAPNLGQLYGFYGNPNLDPEKSKQWEGAFEGLTAGVNWRISGYRNDVSDLIDYDDHTLKYYNEGKARIKGVEATANFDTGPLTHTVSYDYV` `___________________________394_______________412___________________________442__________455_____________________________` `______________________________________________________________________________________________________________` `1nqe(A) : DARNAITDTPLLRRAKQQVKYQLDWQLYDFDWGITYQYLGTRYDKDYSSYPYQTVKMGGVSLWDLAVAYPVTSHLTVRGKIANLFDKDYETVYGYQTAGREYTLSGSYTF` `:` `2gsk(A) : DARNAITDTPLLRRAKQQVKYQLDWQLYDFDWGITYQYLGTRYDKDYSSYPYQTVKMGGVSLWDLAVAYPVTSHLTVRGKIANLFDKDYETVYGYQTAGREYTLSGSYTF` `______________________________________________________________________________________________________________`

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)	29.0
Translation (A)	0.2
Closure (%)	76.7
Bending Residues ( green )	394 - 395 397 - 400 412 - 413 442 - 444 455 - 457
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification: Hinge

PyMOL Script

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