DynDom - Protein Domain Motions

DNA Polymerase

(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 Polymerase
Conformer 1 (PDB)	4k8z (A)
Conformer 2 (PDB)	5omf (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	280	0.67	6 - 16 31 - 36 75 - 76 115 - 126 350 - 452 496 - 613 627 - 641 737 - 749
2	238	0.43	3 - 5 17 - 30 127 - 347
3	75	0.35	37 - 74 78 - 114
4	34	0.56	458 - 491
5	106	0.65	616 - 626 642 - 736

Sequence

`____5_________16____________30___35____________________________________73_____________________________________113_______` `4k8z(A) : MILDTDYITEDGKPVIRIFKKENGEFKIEYDRTFEPYFYALLKDDSAIEEVKKITAERHGTVVTVKRVEKVQKKFLGRPVEVWKLYFTHPQDVPAIRDKIREHPAVIDIYEYDIPFAKRY` `:` `5omf(A) : MILDTDYITEDGKPVIRIFKKENGEFKIEYDRTFEPYFYALLKDDSAIEEVKKITAERHGTVVTVKRVEKVQKKFLGRPVEVWKLYFTHPQDVPAIRDKIREHPAVIDIYEYDIPFAKRY` `____5_________16____________30___35____________________________________73_____________________________________113_______` `___126__________________________________________________________________________________________________________________` `4k8z(A) : LIDKGLVPMEGDEELKMLAFAIATLYHEGEEFAEGPILMISYADEEGARVITWKNVDLPYVDVVSTEREMIKRFLRVVKEKDPDVLITYNGDNFDFAYLKKRCEKLGINFALGRDGSEPK` `:` `5omf(A) : LIDKGLVPMEGDEELKMLAFAIATLYHEGEEFAEGPILMISYADEEGARVITWKNVDLPYVDVVSTEREMIKRFLRVVKEKDPDVLITYNGDNFDFAYLKKRCEKLGINFALGRDGSEPK` `___126__________________________________________________________________________________________________________________` `______________________________________________________________________________________________________345_______________` `4k8z(A) : IQRMGDRFAVEVKGRIHFDLYPVIRRTINLPTYTLEAVYEAVFGQPKEKVYAEEITTAWETGENLERVARYSMEDAKVTYELGKEFLPMEAQLSRLIGQSLWDVSRSSTGNLVEWFLLRK` `:` `5omf(A) : IQRMGDRFAVEVKGRIHFDLYPVIRRTINLPTYTLEAVYEAVFGQPKEKVYAEEITTAWETGENLERVARYSMEDAKVTYELGKEFLPMEAQLSRLIGQSLWDVSRSSTGNLVEWFLLRK` `______________________________________________________________________________________________________345_______________` `_________________________________________________________________________________________452____________________________` `4k8z(A) : AYERNELAPNKPDEKELARRRQSYEGGYVKEPERGLWENIVYLDFRSLYPSIIITHNVSPDTLNREGCKEYDVAPQVGHRFCKDFPGFIPSLLGDLLEERQKIKKKMKATIDPIERKLLD` `:` `5omf(A) : AYERNELAPNKPDEKELARRRQSYEGGYVKEPERGLWENIVYLDFRSLYPSIIITHNVSPDTLNREGCKEYDVAPQVGHRFCKDFPGFIPSLLGDLLEERQKIKKKMKATIDPIERKLLD` `_________________________________________________________________________________________452____________________________` `________491_____________________________________________________________________________________________________________` `4k8z(A) : YRQRAIKILANSYYGYYGYARARWYCKECAESVTAWGREYITMTIKEIEEKYGFKVIYSDTDGFFATIPGADAETVKKKAMEFLKYINAKLPGALELEYEGFYKRGFFVTKKKYAVIDEE` `:` `5omf(A) : YRQRAIKILANSYYGYYGYARARWYCKECAESVTAWGREYITMTIKEIEEKYGFKVIYSDTDGFFATIPGADAETVKKKAMEFLKYINAKLPGALELEYEGFYKRGFFVTKKKYAVIDEE` `________491_____________________________________________________________________________________________________________` `__________613__________626____________641_______________________________________________________________________________` `4k8z(A) : GKITTRGLEIVRRDWSEIAKETQARVLEALLKDGDVEKAVRIVKEVTEKLSKYEVPPEKLVIHEQITRDLKDYKATGPHVAVAKRLAARGVKIRPGTVISYIVLKGSGRIGDRAIPFDEF` `:` `5omf(A) : GKITTRGLEIVRRDWSEIAKETQARVLEALLKDGDVEKAVRIVKEVTEKLSKYEVPPEKLVIHEQITRDLKDYKATGPHVAVAKRLAARGVKIRPGTVISYIVLKGSGRIGDRAIPFDEF` `__________613__________626____________641_______________________________________________________________________________` `_____________736____________________` `4k8z(A) : DPTKHKYDAEYYIENQVLPAVERILRAFGYRKEDLR` `:` `5omf(A) : DPTKHKYDAEYYIENQVLPAVERILRAFGYRKEDLR` `_____________736____________________`

Morph

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Status: Initialising

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Domain Pairs

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( red )	2
Rotation Angle (deg)	5.9
Translation (A)	-0.8
Closure (%)	26.9
Bending Residues ( green )	5 - 6 16 - 17 30 - 31 126 - 127 345 - 357
Bending Region Analysis

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( yellow )	3
Rotation Angle (deg)	6.9
Translation (A)	0.8
Closure (%)	40.8
Bending Residues ( green )	35 - 37 73 - 82 113 - 115
Bending Region Analysis

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( violet )	4
Rotation Angle (deg)	29.5
Translation (A)	-1.2
Closure (%)	92.6
Bending Residues ( green )	452 - 459 491 - 496
Bending Region Analysis

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( cyan )	5
Rotation Angle (deg)	7.8
Translation (A)	-0.1
Closure (%)	88.5
Bending Residues ( green )	613 - 616 626 - 627 641 - 642 736 - 737
Bending Region Analysis