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)	2iw5 (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	556	0.62	174 - 421 508 - 511 515 - 829
2	74	1.15	422 - 507 512 - 514

Sequence

`________________________________________________________________________________________________________________________` `2dw4(A) : SGVEGAAFQSRLPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHGLINFGIYKRIKPLPTKKTGKVIIIGSGVSG` `:` `2iw5(A) : PSGVEGAAFQSRLPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHGLINFGIYKRIKPLPTKKTGKVIIIGSGVSG` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `2dw4(A) : LAAARQLQSFGMDVTLLEARDRVGGRVATFRKGNYVADLGAMVVTGLGGNPMAVVSKQVNMELAKIKQKCPLYEANGQAVPKEKDEMVEQEFNRLLEATSYLSHQLDFNVLNNKPVSLGQ` `:` `2iw5(A) : LAAARQLQSFGMDVTLLEARDRVGGRVATFRKGNYVADLGAMVVTGLGGNPMAVVSKQVNMELAKIKQKCPLYEANGQAVPKEKDEMVEQEFNRLLEATSYLSHQLDFNVLNNKPVSLGQ` `________________________________________________________________________________________________________________________` `________421___________________________________________________________________________________507____514________________` `2dw4(A) : ALEVVIQLQEKHVKDEQIEHWKKIVKTQEELKELLNKMVNLKEKIKELH---------------tAEFLVKSKHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDVYLSSRDRQILD` `:` `2iw5(A) : ALEVVIQLQEKHVKDEQIEHWKKIVKTQEELKELLNKMVNLKEKIKELHQQYKEASEVKPPRDITAEFLVKSKHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDVYLSSRDRQILD` `________421___________________________________________________________________________________507____514________________` `________________________________________________________________________________________________________________________` `2dw4(A) : WHFANLEFANATPLSTLSLKHWDQDDDFEFTGSHLTVRNGYSCVPVALAEGLDIKLNTAVRQVRYTASGCEVIAVNTRSTSQTFIYKCDAVLCTLPLGVLKQQPPAVQFVPPLPEWKTSA` `:` `2iw5(A) : WHFANLEFANATPLSTLSLKHWDQDDDFEFTGSHLTVRNGYSCVPVALAEGLDIKLNTAVRQVRYTASGCEVIAVNTRSTSQTFIYKCDAVLCTLPLGVLKQQPPAVQFVPPLPEWKTSA` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `2dw4(A) : VQRMGFGNLNKVVLCFDRVFWDPSVNLFGHVGSTTASRGELFLFWNL--aPILLALVAGEAAGIMENISDDVIVGRCLAILKGIFGSSAVPQPKETVVSRWRADPWARGSYSYVAAGSSG` `:` `2iw5(A) : VQRMGFGNLNKVVLCFDRVFWDPSVNLFGHVGSTTASRGELFLFWNLYKAPILLALVAGEAAGIMENISDDVIVGRCLAILKGIFGSSAVPQPKETVVSRWRADPWARGSYSYVAAGSSG` `________________________________________________________________________________________________________________________` `__________________________________________________________________` `2dw4(A) : NDYDLMAQPITP---------pIPRLFFAGEHTIRNYPATVHGALLSGLREAGRIADQFLG****` `:` `2iw5(A) : NDYDLMAQPITPGPSIPGAPQPIPRLFFAGEHTIRNYPATVHGALLSGLREAGRIADQFLGAMYTL` `__________________________________________________________________`

Morph

This morph was created using the MorphIt_Pro protein morphing technique.
For more advanced options, right click on the model.

play backwards

pause

play forwards

Domain Pairs

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( red )	2
Rotation Angle (deg)	9.5
Translation (A)	1.3
Closure (%)	99.7
Bending Residues ( green )	421 - 422 507 - 508 510 - 512 514 - 519
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification: Shear

PyMOL Script

Download and extract PyMOL PML script file

Download