DynDom - Protein Domain Motions

Lactoferrin

(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	Lactoferrin
Conformer 1 (PDB)	1lfh (A)
Conformer 2 (PDB)	1lfi (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	169	0.54	6 - 90 252 - 327 681 - 683 685 - 689
2	159	0.62	92 - 250
3	354	1.01	328 - 680 684 - 684

Sequence

`_________________________________________________________________________________83_____________________________________` `1lfh(A) : GRRRSVQWCAVSNPEATKCFQWQRNMRKVRGPPVSCIKRDSPIQCIQAIAENRADAVTLDGGFIYEAGLAPYKLRPVAAEVYGTERQPRTHYYAVAVVKKGGSFQLNELQGLKSCHTGLR` `:` `1lfi(A) : GRRRSVQWCAVSNPEATKCFQWQRNMRKVRGPPVSCIKRDSPIQCIQAIAENRADAVTLDGGFIYEAGLAPYKLRPVAAEVYGTERQPRTHYYAVAVVKKGGSFQLNELQGLKSCHTGLR` `_________________________________________________________________________________83_____________________________________` `________________________________________________________________________________________________________________________` `1lfh(A) : RTAGWNVPIGTLRPFLNWTGPPEPIEAAVARFFSASCVPGADKGQFPNLCRLCAGTGENKCAFSSQEPYFSYSGAFKCLKDGAGDVAFIRESTVFEDLSDEAERDEYELLCPDNTRKPVD` `:` `1lfi(A) : RTAGWNVPIGTLRPFLNWTGPPEPIEAAVARFFSASCVPGADKGQFPNLCRLCAGTGENKCAFSSQEPYFSYSGAFKCLRDGAGDVAFIRESTVFEDLSDEAERDEYELLCPDNTRKPVD` `________________________________________________________________________________________________________________________` `______249___________________________________________________________________________327_________________________________` `1lfh(A) : KFKDCHLARVPSHAVVARSVNGKEDAIWNLLRQAQEKFGKDKSPKFQLFGSPSGQKDLLFKDSAIGFSRVPPRIDSGLYLGSGYFTAIQNLRKSEEEVAARRARVVWCAVGEQELRKCNQ` `:` `1lfi(A) : KFKDCHLARVPSHAVVARSVNGKEDAIWNLLRQAQEKFGKDKSPKFQLFGSPSGQKDLLFKDSAIGFSRVPPRIDSGLYLGSGYFTAIQNLRKSEEEVAARRARVVWCAVGEQELRKCNQ` `______249___________________________________________________________________________327_________________________________` `________________________________________________________________________________________________________________________` `1lfh(A) : WSGLSEGSVTCSSASTTEDCIALVLKGEADAMSLDGGYVYTAGKCGLVPVLAENYKSQQSSDPDPNCVDRPVEGYLAVAVVRRSDTSLTWNSVKGKKSCHTAVDRTAGWNIPMGLLFNQT` `:` `1lfi(A) : WSGLSEGSVTCSSASTTEDCIALVLKGEADAMSLDGGYVYTAGKCGLVPVLAENYKSQQSSDPDPNCVDRPVEGYLAVAVVRRSDTSLTWNSVKGKKSCHTAVDRTAGWNIPMGLLFNQT` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1lfh(A) : GSCKFDEYFSQSCAPGSDPRSNLCALCIGDEEGENKCVPNSNERYYGYTGAFRCLAENAGDVAFVKDVTVLQNTDGNNNEAWAKDLKLADFALLCLDGKRKPVTEARSCHLAMAPNHAVV` `:` `1lfi(A) : GSCKFDEYFSQSCAPGSDPRSNLCALCIGDEEGENKCVPNSNERYYGYTGAFRCLAENAGDVAFVKDVTVLQNTDGNNNEAWAKDLKLADFALLCLDGKRKPVTEARSCHLAMAPNHAVV` `________________________________________________________________________________________________________________________` `_____________________________________________________________________________680___________` `1lfh(A) : SRMDKVERLKQVLLHQQAKFGRNGSDCPDKFCLFQSETKNLLFNDNTECLARLHGKTTYEKYLGPQYVAGITNLKKCSTSPLLEACEFLRK` `:` `1lfi(A) : SRMDKVERLKQVLLHQQAKFGRNGSDCPDKFCLFQSETKNLLFNDNTECLARLHGKTTYEKYLGPQYVAGITNLKKCSTSPLLEACEFLRK` `_____________________________________________________________________________680___________`

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)	54.6
Translation (A)	-0.9
Closure (%)	74.0
Bending Residues ( green )	83 - 92 249 - 252
Bending Region Analysis

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( yellow )	3
Rotation Angle (deg)	8.2
Translation (A)	-0.4
Closure (%)	16.1
Bending Residues ( green )	327 - 328 680 - 681 683 - 685
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification: Hinge

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

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

Movement classification: Mixed

PyMOL Script

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