DynDom - Protein Domain Motions

Abc Transporter, Substrate-Binding Protein

(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	Abc Transporter, Substrate-Binding Protein
Conformer 1 (PDB)	5g61 (A)
Conformer 2 (PDB)	5g5y (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	274	0.49	168 - 349 443 - 534
2	212	0.82	49 - 167 350 - 442

Sequence

`________________________________________________________________________________________________________________________` `5g61(A) : KTLKFMTASSPLSPKDPNEKLILQRLEKETGVHIDWTNYQSDFAEKRNLDISSGDLPDAIHNDGASDVDLMNWAKKGVIIPVEDLIDKYMPNLKKILDEKPEYKALMTAPDGHIYSFP` `:` `5g5y(A) : GPKTLKFMTASSPLSPKDPNEKLILQRLEKETGVHIDWTNYQSDFAEKRNLDISSGDLPDAIHNDGASDVDLMNWAKKGVIIPVEDLIDKYMPNLKKILDEKPEYKALMTAPDGHIYSFP` `________________________________________________________________________________________________________________________` `167_____________________________________________________________________________________________________________________` `5g61(A) : WIEELGDGKESIHSVNDMAWINKDWLKKLGLEMPKTTDDLIKVLEAFKNGDPNGNGEADEIPFSFISGNGNEDFKFLFAAFGIGDNDDHLVVGNDGKVDFTADNDNYKEGVKFIRQLQEK` `:` `5g5y(A) : WIEELGDGKESIHSVNDMAWINKDWLKKLGLEMPKTTDDLIKVLEAFKNGDPNGNGEADEIPFSFISGNGNEDFKFLFAAFGIGDNDDHLVVGNDGKVDFTADNDNYKEGVKFIRQLQEK` `167_____________________________________________________________________________________________________________________` `_____________________________________________________________348________________________________________________________` `5g61(A) : GLIDKEAFEHDWNSYIAKGHDQKFGVYFTWDKNNVTGSNESYDVLPVLAGPSGQKHVARTNGMGFARDKMVITSVNKNLELTAKWIDAQYAPLQSVQNNWGTYGDDKQQNIFELDQASNS` `:` `5g5y(A) : GLIDKEAFEHDWNSYIAKGHDQKFGVYFTWDKNNVTGSNESYDVLPVLAGPSGQKHVARTNGMGFARDKMVITSVNKNLELTAKWIDAQYAPLQSVQNNWGTYGDDKQQNIFELDQASNS` `_____________________________________________________________348________________________________________________________` `___________________________________442__________________________________________________________________________________` `5g61(A) : LKHLPLNGTAPAELRQKTEVGGPLAILDSYYGKVTTMPDDAKWRLDLIKEYYVPYMSNVNNYPRVFMTQEDLDKIAHIEADMNDYIYRKRAEWIVNGNIDTEWDDYKKELEKYGLSDYLA` `:` `5g5y(A) : LKHLPLNGTAPAELRQKTEVGGPLAILDSYYGKVTTMPDDAKWRLDLIKEYYVPYMSNVNNYPRVFMTQEDLDKIAHIEADMNDYIYRKRAEWIVNGNIDTEWDDYKKELEKYGLSDYLA` `___________________________________442__________________________________________________________________________________` `______________` `5g61(A) : IKQKYYDQYQAN` `:` `5g5y(A) : IKQKYYDQYQANKN` `______________`

Morph

Jmol._Canvas2D (Jmol) "jmolApplet"[x]

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)	29.9
Translation (A)	0.5
Closure (%)	99.6
Bending Residues ( green )	167 - 169 348 - 350 442 - 447
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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