DynDom - Protein Domain Motions

Succinyl-Coa:3-Ketoacid-Coenzyme A Transferase

(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	Succinyl-Coa:3-Ketoacid-Coenzyme A Transferase
Conformer 1 (PDB)	1o9l (D)
Conformer 2 (PDB)	1o9l (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	312	0.39	42 - 124 131 - 167 185 - 280 315 - 392 411 - 414 424 - 428 430 - 434 458 - 459 465 - 466
2	23	0.61	125 - 130 168 - 184
3	123	0.53	281 - 314 393 - 410 415 - 423 429 - 429 435 - 457 460 - 464 467 - 516

Sequence

`_________________________________________________________________________115____________130_____________________________` `1o9l(D) : TKFYTDAVEAVKDIPNGATVLVGGFGLCGIPENLIGALLKTGVKELTAVSNNAGVDNFGLGLLLQSKQIKRMISSYVGENAEFERQYLAGELEVELTPQGTLAERIRAGGAGVPAFYTST` `:` `1o9l(A) : TKFYTDAVEAVKDIPNGATVLVGGFGLCGIPENLIGALLKTGVKELTAVSNNAGVDNFGLGLLLQSKQIKRMISSYVGENAEFERQYLAGELEVELTPQGTLAERIRAGGAGVPAFYTST` `_________________________________________________________________________115____________130_____________________________` `__164_________________184_____________________________________________________________________________________________28` `1o9l(D) : GYGTLVQEGGSPIKYNKDGSIAIASKPREVREFNGQHFILEEAIRGDFALVKAWKADQAGNVTFRKSARNFNLPMCKAAETTVVEVEEIVDIGSFAPEDIHIPKIYVHRLVKGEKYEKRI` `:` `1o9l(A) : GYGTLVQEGGSPIKYNKDGSIAIASKPREVREFNGQHFILEEAIRGDFALVKAWKADQAGNVTFRKSARNFNLPMCKAAETTVVEVEEIVDIGSFAPEDIHIPKIYVHRLVKGEKYEKRI` `__164_________________184_____________________________________________________________________________________________28` `0__________________314___________________________________________________________________________392_____________408____` `1o9l(D) : ERL----nVRERIIKRAALEFEDGMYANLGIGIPLLASNFISPNMTVHLQSENGILGLGPYPLQNEVDADLINAGKETVTVLPGASYFSSDESFAMIRGGHVNLTMLGAMQVSKYGDLAN` `:` `1o9l(A) : ERLSVRKnVRERIIKRAALEFEDGMYANLGIGIPLLASNFISPNMTVHLQSENGILGLGPYPLQNEVDADLINAGKETVTVLPGASYFSSDESFAMIRGGHVNLTMLGAMQVSKYGDLAN` `0__________________314___________________________________________________________________________392_____________408____` `________423__428_432______________________457___463_________________________________________________________` `1o9l(D) : WMIPGKLVKGMGGAMDLVSSAKTKVVVTMEHSAKGNAHKIMEKCTLPLTGKQCVNRIITEKAVFDVDRKKGLTLIELWEGLTVDDIKKSTGCDFAVSPKLIPMQQVTT` `:` `1o9l(A) : WMIPGKLVKGMGGAMDLVSSAKTKVVVTMEHSAKGNAHKIMEKCTLPLTGKQCVNRIITEKAVFDVDRKKGLTLIELWEGLTVDDIKKSTGCDFAVSPKLIPMQQVTT` `________423__428_432______________________457___463_________________________________________________________`

Morph

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

Show console

play backwards

pause

play forwards

Domain Pairs

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( red )	2
Rotation Angle (deg)	15.5
Translation (A)	-0.2
Closure (%)	96.9
Bending Residues ( green )	115 - 125 130 - 132 164 - 170 184 - 185
Bending Region Analysis

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( yellow )	3
Rotation Angle (deg)	5.2
Translation (A)	0.6
Closure (%)	99.9
Bending Residues ( green )	280 - 281 314 - 315 392 - 393 408 - 421 423 - 424 428 - 430 432 - 435 457 - 460 463 - 467
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: Shear

PyMOL Script

Download and extract PyMOL PML script file