DynDom - Protein Domain Motions

Phosphoglucomutase 1

(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	Phosphoglucomutase 1
Conformer 1 (PDB)	1kfi (A)
Conformer 2 (PDB)	1kfi (B)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	233	0.37	129 - 130 208 - 210 213 - 238 245 - 264 267 - 308 311 - 370 380 - 402 406 - 448 529 - 542
2	216	0.29	5 - 128 131 - 207 211 - 212 239 - 244 265 - 266 309 - 310 403 - 405
3	117	0.35	371 - 379 449 - 528 543 - 570

Sequence

`________________________________________________________________________________________________________________________` `1kfi(A) : QVIPAPRVQVTQPYAGQKPGTSGLRKKVSEATQPNYLENFVQSIFNTLRKDELKPKNVLFVGGDGRYFNRQAIFSIIRLAYANDISEVHVGQAGLMSTPASSHYIRKVNEEVGNCIGGII` `:` `1kfi(B) : QVIPAPRVQVTQPYAGQKPGTSGLRKKVSEATQPNYLENFVQSIFNTLRKDELKPKNVLFVGGDGRYFNRQAIFSIIRLAYANDISEVHVGQAGLMSTPASSHYIRKVNEEVGNCIGGII` `________________________________________________________________________________________________________________________` `___128____________________________________________________________________________207____________________________238___2` `1kfi(A) : LTASHNPGGKEHGDFGIKFNVRTGAPAPEDFTDQIYTHTTKIKEYLTVDYEFEKHINLDQIGVYKFEGTRLEKSHFEVKVVDTVQDYTQLMQKLFDFDLLKGLFSNKDFSFRFDGMHGVA` `:` `1kfi(B) : LTASHNPGGKEHGDFGIKFNVRTGAPAPEDFTDQIYTHTTKIKEYLTVDYEFEKHINLDQIGVYKFEGTRLEKSHFEVKVVDTVQDYTQLMQKLFDFDLLKGLFSNKDFSFRFDGMHGVA` `___128____________________________________________________________________________207____________________________238___2` `44_________________264_________________________________________308______________________________________________________` `1kfi(A) : GPYAKHIFGTLLGCSKESLLNCDPSEDFGGGHPDPNLTYAHDLVELLDIHKKKDVGTVPQFGAACDGDADRNMILGRQFFVTPSDSLAVIAANANLIFKNGLLGAARSMPTSGALDKVAA` `:` `1kfi(B) : GPYAKHIFGTLLGCSKESLLNCDPSEDFGGGHPDPNLTYAHDLVELLDIHKKKDVGTVPQFGAACDGDADRNMILGRQFFVTPSDSLAVIAANANLIFKNGLLGAARSMPTSGALDKVAA` `44_________________264_________________________________________308______________________________________________________` `_____370______379____________________402___________________________________________448__________________________________` `1kfi(A) : KNGIKLFETPTGWKFFGNLMDAGLINLCGEESFGTGSNHIREKDGIWAVLAWLTILAHKNKNTDHFVTVEEIVTQYWQQFGRNYYSRYDYEQVDSAGANKMMEHLKTKFQYFEQLKQGNK` `:` `1kfi(B) : KNGIKLFETPTGWKFFGNLMDAGLINLCGEESFGTGSNHIREKDGIWAVLAWLTILAHKNKNTDHFVTVEEIVTQYWQQFGRNYYSRYDYEQVDSAGANKMMEHLKTKFQYFEQLKQGNK` `_____370______379____________________402___________________________________________448__________________________________` `___________________________________________528___________542______________________________` `1kfi(A) : ADIYDYVDPVDQSVSKNQGVRFVFGDGSRIIFRLSGTGSVGATIRIYFEQFEQQQIQHETATALANIIKLGLEISDIAQFTGRNEPTVIT` `:` `1kfi(B) : ADIYDYVDPVDQSVSKNQGVRFVFGDGSRIIFRLSGTGSVGATIRIYFEQFEQQQIQHETATALANIIKLGLEISDIAQFTGRNEPTVIT` `___________________________________________528___________542______________________________`

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)	4.7
Translation (A)	-0.1
Closure (%)	95.2
Bending Residues ( green )	128 - 131 207 - 208 210 - 213 238 - 239 244 - 245 264 - 267 308 - 313 402 - 406
Bending Region Analysis

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( yellow )	3
Rotation Angle (deg)	4.9
Translation (A)	-0.1
Closure (%)	99.9
Bending Residues ( green )	370 - 371 379 - 380 448 - 449 528 - 529 542 - 543
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification: Shear

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

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

Movement classification: Shear

PyMOL Script

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