DynDom - Protein Domain Motions

Lethal Factor

(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
Conformer 1 (PDB)	1yqy (A)
Conformer 2 (PDB)	1pwq (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	31	8.8	437 - 467
2	21	6.53	416 - 436
3	74	17.39	551 - 594 603 - 632
4	31	4.96	385 - 415
5	23	7.54	595 - 602 677 - 691

Sequence

`________________________________________________________________________________________________________________________` `1yqy(A) : ************************************LSRYEKWEKIKQHYQHWSDSLSEEGRGLLKKLQIPIEPKKDDIIHSLSQEEKELLKRIQIDSSDFLSTEEKEFLKKLQIDIR` `:` `1pwq(A) : ERNKTQEEHLKEIMKHIVKIEVKGEEAVKKEAAEKLLEKVPSDVLEMYKAIGGKIYIVDGDITKHISLEALSEDKKKIKDIYGKDALLHEHYVYAKEGYEPVLVIQSSEDYVENTEKALN` `________________________________________________________________________________________________________________________` `__________________________________________________________________415__________________436____________________________46` `1yqy(A) :` `DSLSEEEKELLNRIQVDSSNPLSEKEKEFLKKLKLDIQPYDINQRLQDTGGLIDSPSINLDVRKQYKRDIQNIDALLHQSIGSTLYNKIYLYENMNINNLTATLGADLVDSTDNTKINRG` `:` `1pwq(A) :` `------------------VYYEIGKILSRDILSKINQPYQKFLDVLNTIKNASDSDGQDLLFTNQLKEHPTDFSVEFLEQNSNEVQEVFAKAFAYYIEPQHRDVLQLYAPEAFNYMDKFN` `__________________________________________________________________197__________________218____________________________24` `7_______________________________________________________________________________________________________________________` `1yqy(A) : IFNEFKKNFKYSISSNYMIVDINERPALDNERLKWRIQLSPDTRAGYLENGKLILQRNIGLEIKDVQIIKQSEKEYIRIDAKVVPKSKIDTKIQEAQLNINQEWNKALGLPKYTKLITFN` `:` `1pwq(A) : EQEINLSLEELKDQRMLSRYEKWEKIKQHYQHWSDSLSEEGRGLLKKLQIPIEPKKDDIIHSLSQEEKELLKRIQIDSSDFLSTEEKEFLKKLQIDIRsNPLSEKEKEFLKKLKLDIQPY` `9_______________________________________________________________________________________________________________________` `_____594_____602___________________________632__________________________________________________________________________` `1yqy(A) : VHNRYASNIVESAYLILNEWKNNIQSDLIKKVTNYLVDGNGRFVFTDITLPNIAEQYTHQDEIYEQVHSKGLYVPESRSILLHGPSKGVELRNDSEGFIHEFGHAVDDYAGYLLDKNQSD` `:` `1pwq(A) : DINQRLQDTGGLIDSPSINLDVRKQYKRDIQNIDALLHQSIGSTLYNKIYLYENMNINNLTATLGADLVDSTDNTKINRGIFNEFKKNFKYSISSNYMIVDINERPALDNERLKWRIQLS` `_____394_____402___________________________432__________________________________________________________________________` `________________________________________________________________________________________________________________________` `1yqy(A) : LVTNSKKFIDIFKEEGSNLTSYGRTNEAEFFAEAFRLMHSTDHAERLKVQKNAPKTFQFINDQIKFIINSLV********************************************` `:` `1pwq(A) : PDTRAGYLENGKLILQRNIGLEIKDVQIIKQSEKEYIRIDAKVVPKSKIDTKIQEAQLNINQEWNKALGLPKYTKLITFNVHNRYASNIVESAYLILNEWKNNIQSDLIKKVTNYLVDGN` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1yqy(A) : ********************************************************************************************************************` `:` `1pwq(A) : GRFVFTDITLPNIAEQYTHQDEIYEQVHSKGLYVPESRSILLHGPSKGVELRNDSEGFIHEFGHAVDDYAGYLLDKNQSDLVTNSKKFIDIFKEEGSNLTSYGRTNEAEFFAEAFRLMHS` `________________________________________________________________________________________________________________________` `______________________________` `1yqy(A) : ****************************` `:` `1pwq(A) : TDHAERLKVQKNAPKTFQFINDQIKFIINS` `______________________________`

Morph

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Status: Initialising

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	156.1	14.5	25.8	436 - 437	Bending Region Analysis
1	3	76.6	-60.2	73.5	467 - 551	Bending Region Analysis
4	2	145.8	3.1	80.2	415 - 416	Bending Region Analysis
3	5	176.6	-9.6	78.2	594 - 595 602 - 603 632 - 677	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

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

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

Movement classification:

No Contacts

Conformer 1 Contact:
Residue 3 ———› Residue 5

Conformer 2 Contact:
Residue 5 ———› Residue 3

Movement classification: Hinge

PyMOL Script

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