DynDom - Protein Domain Motions

Lysine-Specific Histone Demethylase 1

(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	Lysine-Specific Histone Demethylase 1
Conformer 1 (PDB)	2dw4 (A)
Conformer 2 (PDB)	2uxn (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	551	0.57	175 - 421 515 - 829
2	78	1.17	422 - 514

Sequence

`________________________________________________________________________________________________________________________` `2dw4(A) : SGVEGAAFQSRLPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHGLINFGIYKRIKPLPTKKTGKVIIIGSGVSGL` `:` `2uxn(A) : GVEGAAFQSRLPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHGLINFGIYKRIKPLPTKKTGKVIIIGSGVSGL` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `2dw4(A) : AAARQLQSFGMDVTLLEARDRVGGRVATFRKGNYVADLGAMVVTGLGGNPMAVVSKQVNMELAKIKQKCPLYEANGQAVPKEKDEMVEQEFNRLLEATSYLSHQLDFNVLNNKPVSLGQA` `:` `2uxn(A) : AAARQLQSFGMDVTLLEARDRVGGRVATFRKGNYVADLGAMVVTGLGGNPMAVVSKQVNMELAKIKQKCPLYEANGQAVPKEKDEMVEQEFNRLLEATSYLSHQLDFNVLNNKPVSLGQA` `________________________________________________________________________________________________________________________` `_______421__________________________________________________________________________________________514_________________` `2dw4(A) : LEVVIQLQEKHVKDEQIEHWKKIVKTQEELKELLNKMVNLKEKIKELH---------------tAEFLVKSKHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDVYLSSRDRQILDW` `:` `2uxn(A) : LEVVIQLQEKHVKDEQIEHWKKIVKTQEELKELLNKMVNLKEKIKELHQQYKEASEVKPPRDITAEFLVKSKHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDVYLSSRDRQILDW` `_______421__________________________________________________________________________________________514_________________` `________________________________________________________________________________________________________________________` `2dw4(A) : HFANLEFANATPLSTLSLKHWDQDDDFEFTGSHLTVRNGYSCVPVALAEGLDIKLNTAVRQVRYTASGCEVIAVNTRSTSQTFIYKCDAVLCTLPLGVLKQQPPAVQFVPPLPEWKTSAV` `:` `2uxn(A) : HFANLEFANATPLSTLSLKHWDQDDDFEFTGSHLTVRNGYSCVPVALAEGLDIKLNTAVRQVRYTASGCEVIAVNTRSTSQTFIYKCDAVLCTLPLGVLKQQPPAVQFVPPLPEWKTSAV` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `2dw4(A) : QRMGFGNLNKVVLCFDRVFWDPSVNLFGHVGSTTASRGELFLFWNL--aPILLALVAGEAAGIMENISDDVIVGRCLAILKGIFGSSAVPQPKETVVSRWRADPWARGSYSYVAAGSSGN` `:` `2uxn(A) : QRMGFGNLNKVVLCFDRVFWDPSVNLFGHVGSTTASRGELFLFWNLYKAPILLALVAGEAAGIMENISDDVIVGRCLAILKGIFGSSAVPQPKETVVSRWRADPWARGSYSYVAAGSSGN` `________________________________________________________________________________________________________________________` `_________________________________________________________________` `2dw4(A) : DYDLMAQPITP---------pIPRLFFAGEHTIRNYPATVHGALLSGLREAGRIADQFLG****` `:` `2uxn(A) : DYDLMAQPITPGPSIPGAPQPIPRLFFAGEHTIRNYPATVHGALLSGLREAGRIADQFLGAMYTL` `_________________________________________________________________`

Morph

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

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( red )	2
Rotation Angle (deg)	9.7
Translation (A)	1.2
Closure (%)	99.5
Bending Residues ( green )	421 - 422 514 - 519
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification:

No Contacts

PyMOL Script

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