DynDom - Protein Domain Motions

Maltose Transport System Permease Protein Malf

(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	Maltose Transport System Permease Protein Malf
Conformer 1 (PDB)	2r6g (F)
Conformer 2 (PDB)	3pv0 (F)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	45	1.72	87 - 92 258 - 261 266 - 268 275 - 277 449 - 449 471 - 471 473 - 475 477 - 477 480 - 502
2	61	1.08	20 - 80
3	160	1.56	93 - 257
4	206	1.2	262 - 265 269 - 274 278 - 448 450 - 470 472 - 472 476 - 476 478 - 479

Sequence

`__________________________________________________________________80__________92________________________________________` `2r6g(F) : DALKWSVLGLLGLLVGYLVVLMYAQGEYLFAITTLILSSAGLYIFANRKAYAWRYVYPGMAGMGLFVLFPLVCTIAIAFTNYSSTNQLTFERAQEVLLDRSWQAGKTYNFGLYPAGDEWQ` `:` `3pv0(F) : ****SVLGLLGLLVGYLVVLMYAQGEYLFAITTLILSSAGLYIFANRKAYAWRYVYPGMAGMGLFVLFPLVCTIAIAFTNYSSTNQLTFERAQEVLLDRSWQAGKTYNFGLYPAGDEWQ` `__________________________________________________________________80__________92________________________________________` `________________________________________________________________________________________________________________________` `2r6g(F) : LALSDGETGKNYLSDAFKFGGEQKLQLKETTAQPEGERANLRVITQNRQALSDITAILPDGNKVMMSSLRQFSGTQPLYTLDGDGTLTNNQSGVKYRPNNQIGFYQSITAnWGDEKLSPG` `:` `3pv0(F) : LALSDGETGKNYLSDAFKFGGEQKLQLKETTAQPEGERANLRVITQNRQALSDITAILPDGNKVMMSSLRQFSGTQPLYTLDGDGTLTNNQSGVKYRPNNQIGFYQSITA---dEKLSPG` `________________________________________________________________________________________________________________________` `257_261____268___274____________________________________________________________________________________________________` `2r6g(F) : YTVTTGWKNFTRVFTDEGIQKPFLAIFVWTVVFSLITVFLTVAVGMVLACLVQWEALRGKAVYRVLLILPYAVPSFISILIFKGLFNQSFGEINMMLSALFGVKPAWFSDPTTARTMLII` `:` `3pv0(F) : YTVTTGWKNFTRVFTDEGIQKPFLAIFVWTVVFSLITVFLTVAVGMVLACLVQWEALRGKAVYRVLLILPYAVPSFISILIFKGLFNQSFGEINMMLSALFGVKPAWFSDPTTARTMLII` `257_261____268___274____________________________________________________________________________________________________` `_______________________________________________________________________448___________________470__475___________________` `2r6g(F) : VNTWLGYPYMMILCMGLLKAIPDDLYEASAMDGAGPFQNFFKITLPLLIKPLTPLMIASFAFNFNNFVLIQLLTNGGPDRLGTTTPAGYTDLLVNYTYRIAFEGGGGQDFGLAAAIATLI` `:` `3pv0(F) : VNTWLGYPYMMILCMGLLKAIPDDLYEASAMDGAGPFQNFFKITLPLLIKPLTPLMIASFAFNFNNFVLIQLLTNGGPDRLGTTTPAGYTDLLVNYTYRIAFEGGGGQDFGLAAAIATLI` `_______________________________________________________________________448___________________470__475___________________` `___________` `2r6g(F) : FLLVGALAIV` `:` `3pv0(F) : FLLVGALAIVN` `___________`

Morph

This morph was created using the MorphIt_Pro protein morphing technique.
For more advanced options, right click on the model.

Show console

play backwards

pause

play forwards

Domain Pairs

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( red )	2
Rotation Angle (deg)	14.1
Translation (A)	-3.1
Closure (%)	85.1
Bending Residues ( green )	80 - 87
Bending Region Analysis

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( yellow )	3
Rotation Angle (deg)	19.1
Translation (A)	1.4
Closure (%)	59.7
Bending Residues ( green )	92 - 93 257 - 258
Bending Region Analysis

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( violet )	4
Rotation Angle (deg)	16.9
Translation (A)	0.9
Closure (%)	90.5
Bending Residues ( green )	261 - 266 268 - 271 274 - 275 277 - 278 448 - 452 470 - 473 475 - 483
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification:

No Contacts

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

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

Movement classification: Shear

Conformer 1 Contact:
Residue 1 ———› Residue 4

Conformer 2 Contact:
Residue 4 ———› Residue 1

Movement classification: Shear

PyMOL Script

Download and extract PyMOL PML script file

Maltose Transport System Permease Protein Malf

DynDom run details

Domains

Sequence

Morph

Domain Pairs

Dynamic Contact Graph

Full-size image

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

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

Movement classification:

No Contacts

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

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

Movement classification: Shear

Conformer 1 Contact:Residue 1 ———› Residue 4

Conformer 2 Contact:Residue 4 ———› Residue 1

Movement classification: Shear

PyMOL Script

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

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

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

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

Conformer 1 Contact:
Residue 1 ———› Residue 4

Conformer 2 Contact:
Residue 4 ———› Residue 1