DynDom - Protein Domain Motions

DNA Ligase

(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	DNA Ligase
Conformer 1 (PDB)	6wbo (A)
Conformer 2 (PDB)	3rr5 (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	221	0.7	203 - 207 209 - 210 219 - 220 224 - 435
2	201	1.51	14 - 202 208 - 208 211 - 218 221 - 223
3	127	0.85	436 - 562

Sequence

`________________________________________________________________________________________________________________________` `6wbo(A) : HMRYSELAELYRRLEKTTLKTLKTKFVADFLKKTPDDLLEIVPYLILGKVFPDWDERELGVGEKLLIKAVSMATGVPEKEIENSIKDTGDLGESVALALKKRRQKSFFSQPLTIKRVYNT` `:` `3rr5(A) : SKYSELADLYRRLEKTTLKTLKTKFVADFLKKTPDELLEVVPYLILGKVFPDWDERELGVGEKLLIKAVSMATGVPEKEIENSIKDTGDLGESVALALKKRKQKSFFSQPLTIKRVYST` `________________________________________________________________________________________________________________________` `_____________________________________________________________________202__207________218__223___________________________` `6wbo(A) : FVKVAEASGEGSQDRKMKYLANLFMDAGPEEGKYIARTVLGTMRTGVAEGILRDAIAEAFKVKVELVERAYMLTSDFGYVAKIAKLEGNEGLSKVSIQIGKPIRPMLAQNAASVKDALIE` `:` `3rr5(A) : FVKVAEASGEGSQDRKMKYLANLFMDAQPEEGKYIARTVLGTMRTGVAEGILRDAIAEAFRVKPELVERAYMLTSDFGYVAKVAKLEGNEGLSKVSIQIGKPIRPMLAQNAASVKEALIE` `_____________________________________________________________________202__207________218__223___________________________` `________________________________________________________________________________________________________________________` `6wbo(A) : MGGEAAFEIKYDGARVQVHRDGDKVIIYSRRLENVTRSIPEIVEAVKASLKPSKVIVEGELVAVGENGRPRPFQYVLRRFRRKYNIEEMIEKIPLELNLFDILYVNGESLIDTKFTERRK` `:` `3rr5(A) : MGGEAAFEIKYDGARVQVHRDGDRVIIYSRRLENVTRSIPEIVEAVKASLKPSKVIVEGELVAVGENGRPRPFQYVLRRFRRKYNIDEMIEKIPLELNLFDILYVDGESLIDTEFVERRK` `________________________________________________________________________________________________________________________` `_____________________________________________________________434________________________________________________________` `6wbo(A) : RLEESVEESDKIKLAEQLVTKKVDEAEEFYKRALELGHEGLMAKRLDAIYEPGNRGKKWLKIKPTMENLDLVIIGAEWGEGRRAHLLGSFLVGAYDPESGEFVPVGKVGSGFTDEDLVEF` `:` `3rr5(A) : RLEESVEESEKIKIAEQLVTKKVEEAEAFYKRALELGHEGLMAKRLDSVYEPGNRGKKWLKIKPTMENLDLVIIGAEWGEGRRAHLLGSFLVAAYDPDSGEFLPVGKVGSGFTDEDLVEF` `_____________________________________________________________434________________________________________________________` `___________________________________________________________________________` `6wbo(A) : TKMLKPLIIREEGKFVEIEPKVVIEVTYQEIQKSPKYKSGFALRFPRYVALRENKSPEEADTIERVAQLYELQER` `:` `3rr5(A) : TKMLKPLILREEGKFVEIEPKVVIEVTYQEIQKSPKYRSGFALRFPRYVALREDKSPEEADTIERIAQLYELQE` `___________________________________________________________________________`

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)	12.2
Translation (A)	0.0
Closure (%)	98.9
Bending Residues ( green )	202 - 203 207 - 211 218 - 221 223 - 224
Bending Region Analysis

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( yellow )	3
Rotation Angle (deg)	70.1
Translation (A)	-0.8
Closure (%)	44.7
Bending Residues ( green )	434 - 437
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: Hinge

PyMOL Script

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