DynDom - Protein Domain Motions

Sec1

(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	Sec1
Conformer 1 (PDB)	1fvf (B)
Conformer 2 (PDB)	1epu (A)
Window Length	7
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	376	0.96	34 - 40 103 - 103 129 - 303 345 - 588
2	112	0.76	5 - 33 41 - 102 104 - 128
3	27	3.25	304 - 344

Sequence

`_____________________________32___________________________________________________________________102___________________` `1fvf(B) : ALKTAVHEKIMNDVVLAVKKNAEWKVLIVDQLSMRMVSACCKMHEIMSEGITLVEDINRRREPLPLLEAVYLITPTEESVKCLMADFQNPDNPQYRGAHIFFTEACPEELFKELCKSTTA` `:` `1epu(A) : ALKTAVHEKI-nDVVLAVKKNAEWKVLIVDQLS--rvSACCK-hEI-sEGITLVEDINRRREPLPLLEAVYLITPTEESVKCL-aDFQNPDNPQYRGAHIFFTEACPEELFKELCKSTTA` `_____________________________32___________________________________________________________________102___________________` `____128_________________________________________________________________________________________________________________` `1fvf(B) : RFIKTLKEINIAFLPYESQIFSLDSPDTFQVYYNPSRAQGGIPNKERCAEQIATLCATLGEYPSVRYRSDFDENASFAQLVQQKLDAYRADDPTMGEGPQKDRSQLLILDRGFDPISPLL` `:` `1epu(A) : RFIKTLKEINIAFLPYESQIFSLDSPDTFQVYYNPSRAQGGIPNKERCAEQIATLCATLGEYPSVRYRSDFDENASFAQLVQQKLDAYRADDPT-gEGPQKDRSQLLILDRGFDPISPLL` `____128_________________________________________________________________________________________________________________` `___________________________________________295______________________________________344_________________________________` `1fvf(B) : HELTFQAMAYDLLPIENDVYKYVeKEVLLDEKDDLWVEMRHQHIAVVSQNVTKKLKQFADEKR----lSQMLKKMPQYQKELSKYSTHLHLAEDCMKQYQQHVDKLCKVEQDLAMGTDAD` `:` `1epu(A) : HELTFQA-aYDLLPIENDVYKY---eVLLDEKDDLWVE-rHQHIAVVSQNVTKKLKQFADEKRgIKDLSQl--KKpQYQKELSKYSTHLHLAEDC-kQYQQHVDKLCKVEQDLA-gTDAD` `___________________________________________295______________________________________344_________________________________` `________________________________________________________________________________________________________________________` `1fvf(B) : GEKIRDHMRNIVPILLDQKISAYDKIRIILLYIIHKGGISEENLAKLVQHAHIPAEEKWIINDMQNLGVPIIQDGGRRKIPQPYHTHNRKERQADHTYQMSRWTPYMKDIMEAAVEDKLD` `:` `1epu(A) : GEKIRDH-rNIVPILLDQKISAYDKIRIILLYIIHKGGISEENLAKLVQHAHIPAEEKWIIND-qNLGVPIIQDGGRRKIPQPYHTHNRKERQADHTYQ-sRWTPY-kDI-eAAVEDKLD` `________________________________________________________________________________________________________________________` `_____________________________________________________________________` `1fvf(B) : TRHYPFLNGGG--gPRLIIFVVGGISYSEMRSAYEVTQTAKNNWEVILGSTHILTPEGLLRDLRKISNP` `:` `1epu(A) : TRHYPFLNGGGkSGPRLIIFVVGGISYSE-rSAYEVTQTAKNNWEVILGSTHILTPEGLLRDLRKISNP` `_____________________________________________________________________`

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)	15.3
Translation (A)	0.6
Closure (%)	6.7
Bending Residues ( green )	32 - 41 102 - 104 128 - 133
Bending Region Analysis

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( yellow )	3
Rotation Angle (deg)	54.5
Translation (A)	2.0
Closure (%)	94.7
Bending Residues ( green )	295 - 304 344 - 345
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification: Hinge

Conformer 1 Contact:
Residue 1 ———› Residue 3

Conformer 2 Contact:
Residue 3 ———› Residue 1

Movement classification:

No Contacts

PyMOL Script

Download and extract PyMOL PML script file

Download