DynDom - Protein Domain Motions

Glucose-1-Phosphate Adenylyltransferase Small Subunit

(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	Glucose-1-Phosphate Adenylyltransferase Small Subunit
Conformer 1 (PDB)	1yp4 (D)
Conformer 2 (PDB)	1yp2 (B)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	133	0.63	17 - 24 66 - 71 106 - 106 118 - 142 149 - 170 183 - 194 228 - 274 292 - 303
2	236	0.52	25 - 65 72 - 105 107 - 112 143 - 148 275 - 291 304 - 449
3	44	0.63	172 - 182 195 - 227

Sequence

`____________24_______________________________________65____71_________________________105______________________________1` `1yp4(D) : *CLDPDASRSVLGIILGGGAGTRLYPLTKKRAKPAVPLGANYRLIDIPVSNCLNSNISKIYVLTQFNSASLNRHLSRAY---eGFVEVLAAQQSPE-qGTADAVRQYLWLFEEHTVLEYL` `:` `1yp2(B) : TCLDPDASRSVLGIIL-----tRLYPLTKKRAKPAVPLGANYRLIDIPVSNCLNSNISKIYVLTQFNSASLNRHLSRAYASNeGFVEVLAAQQSPEfQGTADAVRQYLWLFEEHTVLEYL` `____________24_______________________________________65____71_________________________105______________________________1` `42___148___________________170_________182__________________________________________227_________________________________` `1yp4(D) : ILAGDHLYRMDYEKFIQAHRETDADITVAALPMDEKRATAFGLMKIDEEGRIIEFAEKPQGEQLQAMKVDTTILGLDDKRAKEMPFIASMGIYVISKDVMLNLLRDKFPGANDFGSEVIP` `:` `1yp2(B) : ILAGDHLYRMDYEKFIQAHRETDADITVAALPMDEKRATAFGLMKIDEEGRIIEFAEKPQGEQLQAMKVDTTILGLDDKRAKEMPFIASMGIYVISKDVMLNLLRDKFPGANDFGSEVIP` `42___148___________________170_________182__________________________________________227_________________________________` `___________274______________291____298__________________________________________________________________________________` `1yp4(D) : GATSLGMRVQAYLYDGYWEDIGTIEAFYNANLGITKKPVPDFSFYDRSAPIYTQPRYLPPSKMLDADVTDSVIGEGCVIKNCKIHHSVVGLRSCISEGAIIEDSLLMGADYYETDADRKL` `:` `1yp2(B) : GATSLGMRVQAYLYDGYWEDIGTIEAFYNANLGITKKPVPDFSFYDRSAPIYTQPRYLPPSKMLDADVTDSVIGEGCVIKNCKIHHSVVGLRSCISEGAIIEDSLLMGADYYETDADRKL` `___________274______________291____298__________________________________________________________________________________` `_______________________________________________________________________` `1yp4(D) : LAAKGSVPIGIGKNCHIKRAIIDKNARIGDNVKIINKDNVQEAARETDGYFIKSGIVTVIKDALIPSGIII` `:` `1yp2(B) : LAAKGSVPIGIGKNCHIKRAIIDKNARIGDNVKIINKDNVQEAARETDGYFIKSGIVTVIKDALIPSGIII` `_______________________________________________________________________`

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)	5.0
Translation (A)	0.5
Closure (%)	41.2
Bending Residues ( green )	24 - 25 65 - 66 71 - 72 105 - 118 142 - 143 148 - 149 274 - 275 291 - 292 298 - 304
Bending Region Analysis

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( yellow )	3
Rotation Angle (deg)	20.1
Translation (A)	-0.3
Closure (%)	98.9
Bending Residues ( green )	170 - 172 182 - 195 227 - 228
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: Hinge

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