DynDom - Protein Domain Motions

DNA Polymerase I

(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 I
Conformer 1 (PDB)	1xwl
Conformer 2 (PDB)	1lv5 (B)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	437	0.93	299 - 508 583 - 679 745 - 874
2	74	1.02	509 - 582
3	35	0.51	680 - 714
4	30	0.51	715 - 744

Sequence

`________________________________________________________________________________________________________________________` `1xwl : AKMAFTLADRVTEEMLADKAALVVEVVEENYHDAPIVGIAVVNEHGRFFLRPETALADPQFVAWLGDETKKKSMFDSKRAAVALKWKGIELCGVSFDLLLAAYLLDPAQGVDDVAAAAKM` `:` `1lv5(B) : AKMAFTLADRVTEEMLADKAALVVEVVEENYHAAPIVGIAVVNEHGRFFLRPETALADPQFVAWLGDETKKKSMFDSKRAAVALKWKGIELCGVSFDLLLAAYLLDPAQGVDDVAAAAKM` `________________________________________________________________________________________________________________________` `____________________________________________________________________________________503_________________________________` `1xwl : KQYEAVRPDEAVYGKGAKRAVPDEPVLAEHLVRKAAAIWELERPFLDELRRNEQDRLLVELEQPLSSILAEMEFAGVKVDTKRLEQMGKELAEQLGTVEQRIYELAGQEFNINSPKQLGV` `:` `1lv5(B) : KQYEAVRPDEAVYGKGAKRAVPDEPVLAEHLVRKAAAIWELERPFLDELRRNEQDRLLVELEQPLSSILAEMEFAGVKVDTKRLEQMGKELAEQLGTVEQRIYELAGQEFNINSPKQLGV` `____________________________________________________________________________________503_________________________________` `___________________________________________582__________________________________________________________________________` `1xwl : ILFEKLQLPVLKKTKTGYSTSADVLEKLAPYHEIVENILHYRQLGKLQSTYIEGLLKVVRPDTKKVHTIFNQALTQTGRLSSTEPNLQNIPIRLEEGRKIRQAFVPSESDWLIFAADYSQ` `:` `1lv5(B) : ILFEKLQLPVLKKTKTGYSTSADVLEKLAPYHEIVENILHYRQLGKLQSTYIEGLLKVVRPDTKKVHTIFNQALTQTGRLSSTEPNLQNIPIRLEEGRKIRQAFVPSESDWLIFAADYSQ` `___________________________________________582__________________________________________________________________________` `___________________678_________________________________714___________________________744________________________________` `1xwl : IELRVLAHIAEDDNLMEAFRRDLDIHTKTAMDIFQVSEDEVTPNMRRQAKAVNFGIVYGISDYGLAQNLNISRKEAAEFIERYFESFPGVKRYMENIVQEAKQKGYVTTLLHRRRYLPDI` `:` `1lv5(B) : IELRVLAHIAEDDNLMEAFRRDLDIHTKTAMDIFQVSEDEVTPNMRRQAKAVNFGIVYGISDYGLAQNLNISRKEAAEFIERYFESFPGVKRYMENIVQEAKQKGYVTTLLHRRRYLPDI` `___________________678_________________________________714___________________________744________________________________` `____________________________________________________________________________________________________` `1xwl : TSRNFNVRSFAERMAMNTPIQGSAADIIKKAMIDLNARLKEERLQAHLLLQVHDELILEAPKEEMERLCRLVPEVMEQAVTLRVPLKVDYHYGSTWYDAK` `:` `1lv5(B) : TSRNFNVRSFAERMAMNTPIQGSAADIIKKAMIDLNARLKEERLQAHLLLQVHDELILEAPKEEMERLCRLVPEVMEQAVTLRVPLKVDYHYGSTWYDAK` `____________________________________________________________________________________________________`

Morph

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Status: Initialising

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Domain Pairs

Fixed Domain	Moving Domain	Rotation Angle	Translation (A)	Closure	Bending Residues
1	2	22.3	0.3	32.7	503 - 509 582 - 588	Bending Region Analysis
1	3	44.8	-0.8	88.4	678 - 680	Bending Region Analysis
1	4	12.9	-1.0	90.8	744 - 745	Bending Region Analysis
3	4	42.9	0.1	3.3	714 - 716	Bending Region Analysis

Dynamic Contact Graph

The dynamic contact graph is still being generated. Progress: Initialising

PyMOL Script

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