DynDom - Protein Domain Motions

Lethal Factor Precursor

(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	Lethal Factor Precursor
Conformer 1 (PDB)	1j7n (A)
Conformer 2 (PDB)	1yqy (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	40	10.83	326 - 387
2	56	11.34	163 - 199 246 - 264
3	24	8.09	395 - 403 478 - 492
4	62	11.9	101 - 162

Sequence

`________________________________________________________________________________________________________________________` `1j7n(A) : ERNKTQEEHLKEIMKHIVKIEVKGEEAVKKEAAEKLLEKVPSDVLEMYKAIGGKIYIVDGDITKHISLEALSEDKKKIKDIYGKDALLHEHYVYAKEGYEPVLVIQSSEDYVENTEKAL-` `:` `1yqy(A) : ************************************LSRYEKWEKIKQHYQHWSDSLSEEGRGLLKKLQIPIEPKKDDIIHSLSQEEKELLKRIQIDSSDFLSTEEKEFLKKLQIDIR` `________________________________________________________________________________________________________________________` `___________________________________162__________________________________________________________________________________` `1j7n(A) :` `---------------------NVYYEIGKILSRDILSKINQPYQKFLDVLNTIKNASDSDGQDLLFTNQLKEHPTDFSVEFLEQNSNEVQEVFAKAFAYYIEPQHRDVLQLYAPEAFNYM` `:` `1yqy(A) :` `DSLSEEEKELLNRIQVDSSNPLSEKEKEFLKKLKLDIQPYDINQRLQDTGGLIDSPSINLDVRKQYKRDIQNIDALLHQSIGSTLYNKIYLYENMNINNLTATLGADLVDSTDNTKINRG` `___________________________________384__________________________________________________________________________________` `_________________264__________________________________________________________________________________________________38` `1j7n(A) : DKFNEQEINLSLEELKDQRMLSRYEKWEKIKQHYQHWSDSLSEEGRGLLKKLQIPIEPKKDDIIHSLSQEEKELLKRIQIDSSDFLSTEEKEFLKKLQIDIlSEKEKEFLKKLKLDIQPY` `:` `1yqy(A) : IFNEFKKNFKYSISSNYMIVDINERPALDNERLKWRIQLSPDTRAGYLENGKLILQRNIGLEIKDVQIIKQSEKEYIRIDAKVVPKSKIDTKIQEAQLNINQEWNKALGLPKYTKLITFN` `_________________486__________________________________________________________________________________________________58` `7_______________________________________________________________________________________________________________________` `1j7n(A) : DINQRLQDTGGLIDSPSINLDVRKQYKRDIQNIDALLHQSIGSTLYNKIYLYENMNINNLTATLGADLVDSTDNTKINRGIFNEFKKNFKYSISSNYMIVDINERPALDNERLKWRIQLS` `:` `1yqy(A) : VHNRYASNIVESAYLILNEWKNNIQSDLIKKVTNYLVDGNGRFVFTDITLPNIAEQYTHQDEIYEQVHSKGLYVPESRSILLHGPSKGVELRNDSEGFIHEFGHAVDDYAGYLLDKNQSD` `7_______________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1j7n(A) : PDTRAGYLENGKLILQRNIGLEIKDVQIIKQSEKEYIRIDAKVVPKSKIDTKIQEAQLNINQEWNKALGLPKYTKLITFNVHNRYASNIVESAYLILNEWKNNIQSDLIKKVTNYLVDGN` `:` `1yqy(A) : LVTNSKKFIDIFKEEGSNLTSYGRTNEAEFFAEAFRLMHSTDHAERLKVQKNAPKTFQFINDQIKFIINSLV********************************************` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1j7n(A) : GRFVFTDITLPNIAEQYTHQDEIYEQVHSKGLYVPESRSILLHGPSKGVELRNDSEGFIHEFGHAVDDYAGYLLDKNQSDLVTNSKKFIDIFKEEGSNLTSYGRTNEAEFFAEAFRLMHS` `:` `1yqy(A) : ********************************************************************************************************************` `________________________________________________________________________________________________________________________` `___________________________` `1j7n(A) : TDHAERLKVQKNAPKTFQFINDQIKFI` `:` `1yqy(A) : *************************` `___________________________`

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	106.6	-7.8	74.8	264 - 326	Bending Region Analysis
1	3	146.4	20.8	13.8	387 - 395	Bending Region Analysis
4	2	68.6	-2.8	99.8	162 - 163	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:

No Contacts

Conformer 1 Contact:
Residue 4 ———› Residue 2

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

Movement classification: Hinge

PyMOL Script

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