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)	2ahw (B)
Conformer 2 (PDB)	2ahu (B)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	369	0.47	6 - 276 287 - 290 300 - 300 302 - 306 310 - 319 324 - 372 378 - 378 388 - 410 425 - 436 449 - 449 453 - 456 526 - 526
2	129	0.35	284 - 286 291 - 298 301 - 301 307 - 309 320 - 323 373 - 377 379 - 387 411 - 424 437 - 448 450 - 452 457 - 525 527 - 527

Sequence

`________________________________________________________________________________________________________________________` `2ahw(B) : VKPPRINGRVPVLSAQEAVNYIPDEATLCVLGAGGGILEATTLITALADKYKQTQTPRNLSIISPTGLGDRADRGISPLAQEGLVKWALCGHWGQSPRISDLAEQNKIIAYNYPQGVLTQ` `:` `2ahu(B) : VKPPRINGRVPVLSAQEAVNYIPDEATLCVLGAGGGILEATTLITALADKYKQTQTPRNLSIISPTGLGDRADRGISPLAQEGLVKWALCGHWGQSPRISDLAEQNKIIAYNYPQGVLTQ` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `2ahw(B) : TLRAAAAHQPGIISDIGIGTFVDPRQQGGKLNEVTKEDLIKLVEFDNKEYLYYKAIAPDIAFIRATTCDSEGYATFEDEVMYLDALVIAQAVHNNGGIVMMQVQKMVKKATLHPKSVRIP` `:` `2ahu(B) : TLRAAAAHQPGIISDIGIGTFVDPRQQGGKLNEVTKEDLIKLVEFDNKEYLYYKAIAPDIAFIRATTCDSEGYATFEDEV-yLDALVIAQAVHNNGGIV--qVQK-vKKATLHPKSVRIP` `________________________________________________________________________________________________________________________` `______________________________276_286_________298_____306__________319_323_________________________________________372__` `2ahw(B) : GYLVDIVVVDPDQSQLYGGAPVNRFISGDFTLD-pLNQRKLVARRALFEMRKGAVGNVGVGIADGIGLVAREEGCADDFILTVETGPIGGIT--aNVNTRAILDMTSQFDFYHGGGLDVC` `:` `2ahu(B) : GYLVDIVVVDPDQSQLYGGAPVNRFISGDFTLDlPLNQRKLVARRALFE-rKGAVGNVGVGIADGIGLVAREEGCADDFILTVETGPIGGITSgANVNTRAILD-tSQFDFYHGGGLDVC` `______________________________276_286_________298_____306__________319_323_________________________________________372__` `377_______387____________________410______419______________436_________448_452_456______________________________________` `2ahw(B) : YLSFAEVDQHGNVGVHKFNGKIMGTGGFIDISATSKKIIFCGTLTAGSLKTEIADGKLNIVQEGRVKKFIRELPEITFSGKIALERGLDVRYITERAVFTLKEDGLHLIEIAPGVDLQKD` `:` `2ahu(B) : YLSFAEVDQHGNVGVHKFNGKI-gTGGFIDISATSKKIIFCGTLTAGSLKTEIADGKLNIVQEGRVKKFIRELPEITFSGKIALERGLDVRYITERAVFTLKEDGLHLIEIAPGVDLQKD` `377_______387____________________410______419______________436_________448_452_456______________________________________` `____________________________525____` `2ahw(B) : ILDKMDFTPVISPELKLMDERLFIDAAMGFVLPEA` `:` `2ahu(B) : ILDK-dFTPVISPELKL-dERLFIDAA-gFVLPEA` `____________________________525____`

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)	3.4
Translation (A)	0.0
Closure (%)	99.0
Bending Residues ( green )	276 - 284 286 - 291 298 - 302 306 - 307 309 - 310 319 - 320 323 - 324 372 - 373 377 - 379 387 - 388 410 - 411 419 - 425 436 - 441 448 - 450 452 - 453 456 - 457 525 - 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

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