DynDom - Protein Domain Motions

Polymerase Basic Protein 2

(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	Polymerase Basic Protein 2
Conformer 1 (PDB)	7qtl (C)
Conformer 2 (PDB)	8rmr (C)
Window Length	7
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	277	6.34	252 - 536
2	245	3.07	4 - 251
3	143	1.37	537 - 679
4	42	0.87	693 - 734

Sequence

`________________________________________________________________________________________________________________________` `7qtl(C) : MERIKELRDLMSQSRTREILTKTTVDHMAIIKKYTSGRQEKNPALRMKWMMAMKYPITADKRIMEMIPERNEQGQTLWSKTN---sDRVMVSPLAVTWWNRNGPTTSTVHYPKVYKTYFE` `:` `8rmr(C) : MERIKELRDLMSQSRTREILTKTTVDHMAIIKKYTSGRQEKNPALRMKWMMAMKYPITADKRIMEMIPERNEQRQTLWSKTNDAGSDRVMVSPLAVTWWNRNGPTTSTVHYPKVYKTYFE` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `7qtl(C) : KVERLKHGTFGPVHFRNQVKIRRRVDINPGHADLSAKEAQDVIMEVVFPNEVGARILTSESQLTITKEKKKELQDCKIAPLMVAYMLERELVRKTRFLPVAGGTSSVYIEVLHLTQGTCW` `:` `8rmr(C) : KVERLKHGTFGPVHFRNQVKIRRRVDINPGHADLSAKEAQDVIMEVVFPNEVGARILTSESQLTITKEKKKELQDCKIAPLMVAYMLERELVRKTRFLPVAGGTSSVYIEVLHLTQGTCW` `________________________________________________________________________________________________________________________` `________251_____________________________________________________________________________________________________________` `7qtl(C) : EQMYTPGGEVRNDDVDQSLIIAARNIVRRATVSADPLASLLEMCHSTQIGGVRMVDILRQNPTEEQAVDICKAAMGLRISSSFSFGGFTFKRTSGSSVKREEEVLTGNLQTLKIRVHEGY` `:` `8rmr(C) : EQMYTPGGEVRNDDVDQSLIIAARNIVRRATVSADPLASLLEMCHSTQIGGVRMVDILRQNPTEEQAVDICKAAMGLRISSSFSFGGFTFKRTSGSSVKREEEVLTGNLQTLKIRVHEGY` `________251_____________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `7qtl(C) : EEFTMVGRRATAILRKATRRLIQLIVSGKDEQSIAEAIIVAMVFSQEDCMIKAVRGDLNFVNRANQRLNPMHQLLRHFQKDAKVLFQNWGIEPIDNVMGMIGILPDMTPSTEMSLRGVRV` `:` `8rmr(C) : EEFTMVGRRATAILRKATRRLIQLIVSGKDEQSIAEAIIVAMVFSQEDCMIKAVRGDLNFVNRANQRLNPMHQLLRHFQKDAKVLFQNWGIEPIDNVMGMIGILPDMTPSTEMSLRGVRV` `________________________________________________________________________________________________________________________` `____________________________________________________535_________________________________________________________________` `7qtl(C) : SKM--------eRVVVSIDRFLRVRDQRGNVLLSPEEVSETQGTEKLTITYSSSMMWEINGPESVLVNTYQWIIRNWENVKIQWSQDPTMLYNKMEFEPFQSLVPKAARGQYSGFVRVLF` `:` `8rmr(C) : SKMGVDEYSSTERVVVSIDRFLRVRDQRGNVLLSPEEVSETQGTEKLTITYSSSMMWEINGPESVLVNTYQWIIRNWENVKIQWSQDPTMLYNKMEFEPFQSLVPKAARGQYSGFVRVLF` `____________________________________________________535_________________________________________________________________` `________________________________________________________________________675_____________________________________________` `7qtl(C) : QQMRDVLGTFDTVQIIKLLPFAAAPPEQSRMQFSSLTVNVRGSGMRIVVRGNSPVFNYNKATKRLTVLGKDAGALMEDPDEGTAGVESAVLRGFLILGKENKRYGPALSINELSNLAKGE` `:` `8rmr(C) : QQMRDVLGTFDTVQIIKLLPFAAAPPEQSRMQFSSLTVNVRGSGMRIVVRGNSPVFNYNKATKRLTVLGKDAGALMEDPDEGTAGVESAVLRGFLILGKENKRYGPALSINELSNLAKGE` `________________________________________________________________________675_____________________________________________` `_______________________________________` `7qtl(C) : KANVLIGQGDVVLVMKR**********************` `:` `8rmr(C) : KANVLIGQGDVVLVMKRKRDSSILTDSQTATKRIRMAIN` `_______________________________________`

Morph

This morph was created using the MorphIt_Pro protein morphing technique.
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Domain Pairs

Fixed Domain	Moving Domain	Rotation Angle	Translation (A)	Closure	Bending Residues
1	2	171.9	9.4	54.6	251 - 253	Bending Region Analysis
1	3	124.2	-4.5	59.3	535 - 542	Bending Region Analysis
3	4	106.4	-26.5	53.5	675 - 694	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: Hinge

Conformer 1 Contact:
Residue 3 ———› Residue 4

Conformer 2 Contact:
Residue 4 ———› Residue 3

Movement classification: Hinge

PyMOL Script

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