DynDom - Protein Domain Motions

Putative Enzyme Ydif

(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	Putative Enzyme Ydif
Conformer 1 (PDB)	2ahu (B)
Conformer 2 (PDB)	2ahw (D)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	330	0.34	9 - 275 304 - 304 328 - 372 390 - 410 454 - 456 462 - 462 521 - 526
2	141	0.45	276 - 303 305 - 327 373 - 389 411 - 453 457 - 461 463 - 520 527 - 527

Sequence

`________________________________________________________________________________________________________________________` `2ahu(B) : VKPPRINGRVPVLSAQEAVNYIPDEATLCVLGAGGGILEATTLITALADKYKQTQTPRNLSIISPTGLGDRADRGISPLAQEGLVKWALCGHWGQSPRISDLAEQNKIIAYNYPQGVLTQ` `:` `2ahw(D) : VKPPRINGRVPVLSAQEAVNYIPDEATLCVLGAGGGILEATTLITALADKYKQTQTPRNLSIISPTGLGDRADRGISPLAQEGLVKWALCGHWGQSPRISDLAEQNKIIAYNYPQGVLTQ` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `2ahu(B) : TLRAAAAHQPGIISDIGIGTFVDPRQQGGKLNEVTKEDLIKLVEFDNKEYLYYKAIAPDIAFIRATTCDSEGYATFEDEV-yLDALVIAQAVHNNGGIV--qVQK-vKKATLHPKSVRIP` `:` `2ahw(D) : TLRAAAAHQPGIISDIGIGTFVDPRQQGGKLNEVTKEDLIKLVEFDNKEYLYYKAIAPDIAFIRATTCDSEGYATFEDEVMYLDALVIAQAVHNNGGIVMMQVQKMVKKATLHPKSVRIP` `________________________________________________________________________________________________________________________` `_____________________________275___________________303_____________________327_____________________________________372__` `2ahu(B) : GYLVDIVVVDPDQSQLYGGAPVNRFISGDFTLDlPLNQRKLVARRALFE-rKGAVGNVGVGIADGIGLVAREEGCADDFILTVETGPIGGITSgANVNTRAILD-tSQFDFYHGGGLDVC` `:` `2ahw(D) : GYLVDIVVVDPDQSQLYGGAPVNRFISGDFTLD-pLNQRKLVARRALFEMRKGAVGNVGVGIADGIGLVAREEGCADDFILTVETGPIGGIT--aNVNTRAILDMTSQFDFYHGGGLDVC` `_____________________________275___________________303_____________________327_____________________________________372__` `____________389__________________410________________________________________453_____461_________________________________` `2ahu(B) : YLSFAEVDQHGNVGVHKFNGKI-gTGGFIDISATSKKIIFCGTLTAGSLKTEIADGKLNIVQEGRVKKFIRELPEITFSGKIALERGLDVRYITERAVFTLKEDGLHLIEIAPGVDLQKD` `:` `2ahw(D) : YLSFAEVDQHGNVGVHKFNGKIMGTGGFIDISATSKKIIFCGTLT-----------kLNIVQEG----fI-eLPEITFSGKIALERGLDVRYITERAVFTLKED-lHLIEIAPGVDL---` `____________389__________________410________________________________________453_____461_________________________________` `____________________518___________` `2ahu(B) :` `ILDKdFTPVISPELKL-dERLFIDAA-gFVLPEA` `:` `2ahw(D) :` `----dFTPVISPELKLMDERLFIDAAMGFVLPEA` `____________________518___________`

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)	3.9
Translation (A)	0.0
Closure (%)	99.7
Bending Residues ( green )	275 - 276 303 - 305 327 - 328 372 - 373 389 - 390 410 - 411 453 - 454 456 - 457 461 - 463 518 - 527
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