DynDom - Protein Domain Motions

Endoplasmic Reticulum Aminopeptidase 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	Endoplasmic Reticulum Aminopeptidase 1
Conformer 1 (PDB)	3mdj (A)
Conformer 2 (PDB)	2yd0 (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	165	1.07	401 - 412 438 - 439 518 - 522 525 - 525 527 - 652 655 - 678
2	409	0.83	48 - 400 413 - 437 440 - 517 523 - 524 526 - 526
3	238	1.35	653 - 654 679 - 932

Sequence

`________________________________________________________________________________________________________________________` `3mdj(A) : PFPWNKIRLPEYVIPVHYDLLIHANLTTLTFWGTTKVEITASQPTSTIILHSHHLQISRATLRKGrLSEEPLQVLEHPRQEQIALLAPEPLLVGLPYTVVIHYAGNLSETFHGFYKSTYR` `:` `2yd0(A) : PFPWNKIRLPEYVIPVHYDLLIHANLTTLTFWGTTKVEITASQPTSTIILHSHHLQISRATLRKG-lSEEPLQVLEHPRQEQIALLAPEPLLVGLPYTVVIHYAGNLSETFHGFYKSTYR` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `3mdj(A) : TKEGELRILASTQFEPTAARMAFPCFDEPAFKASFSIKIRREPRHLAISNMPLVKSVTVAEGLIEDHFDVTVKMSTYLVAFIISDFESVSKITKSGVKVSVYAVPDKINQADYALDAAVT` `:` `2yd0(A) : TKEGELRILASTQFEPTAARMAFPCFDEPAFKASFSIKIRREPRHLAISNMPLVKSVTVAEGLIEDHFDVTVKMSTYLVAFIISDFESVSKITKSGVKVSVYAVPDKINQADYALDAAVT` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________395_____________` `3mdj(A) : LLEFYEDYFSIPYPLPKQDLAAIPDFQSGAMENWGLTTYRESALLFDAEKSSASSKLDITMTVAHELAHQWFGNLVTMEWWNDLWLNEGFAKFMEFVSVSVTHPELKVGDYFFGKCFDAM` `:` `2yd0(A) : LLEFYEDYFSIPYPLPKQDLAAIPDFQSGAMENWGLTTYRESALLFDAEKSSASSKLGITMTVAHELAHQWFGNLVTMEWWNDLWLNEGFAKFMEFVSVSVTHPELKVGDYFFGKCFDAM` `________________________________________________________________________________________________________395_____________` `_412__________________________________________________________________________517__522__________________________________` `3mdj(A) : EVDALNSS-----------------dDVSYDKGACILNMLREYLSADAFKSGIVQYLQKHSYKNTKNEDLWDSMASI-vDVKTMMNTWTLQRGFPLITITVRGRNVHMKQEHYMKaPDTG` `:` `2yd0(A) : EVDALNSSHPVSTPVENPAQIREMFDDVSYDKGACILNMLREYLSADAFKSGIVQYLQKHSYKNTKNEDLWDSMASIgVDVKTMMNTWTLQKGFPLITITVRGRNVHMKQEHYMKG-dTG` `_412__________________________________________________________________________517__522__________________________________` `___________________________________________________________________________________646_____________________________678__` `3mdj(A) : YLWHVPLTFITSKSDMVHRFLLKTKTDVLILPEEVEWIKFNVGMNGYYIVHYEDDGWDSLTGLLKGTHTAVSSNDRASLINNAFQLVSIGKLSIEKALDLSLYLKHETEIMPVFQGLNEL` `:` `2yd0(A) : YLWHVPLTFITSKSDMVHRFLLKTKTDVLILPEEVEWIKFNVGMNGYYIVHYEDDGWDSLTGLLKGTHTAVSSNDRASLINNAFQLVSIGKLSIEKALDLSLYLKHETEIMPVFQGLNEL` `___________________________________________________________________________________646_____________________________678__` `________________________________________________________________________________________________________________________` `3mdj(A) : IPMYKLMEKRDMNEVETQFKAFLIRLLRDLIDKQTWTDEGSVSERMLRSELLLLACVHNYQPCVQRAEGYFRKWKESNGNLSLPVDVTLAVFAVGAQSTEGWDFLYSKYQFSLSSTEKSQ` `:` `2yd0(A) : IPMYKLMEKRDMNEVETQFKAFLIRLLRDLIDKQTWTDEGSVSERMLRSQLLLLACVHNYQPCVQRAEGYFRKWKESNGNLSLPVDVTLAVFAVGAQSTEGWDFLYSKYQFSLSSTEKSQ` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `3mdj(A) : IEFALCRTQNKEKLQWLLDESFKGDKIKTQEFPQILTLIGRNPVGYPLAWQFLRKNWNKLVQK----sSSIAHMVMGTTNQFSTRTRLEEVK--------------cVQQTIETIEENIG` `:` `2yd0(A) : IEFALCRTQNKEKLQWLLDESFKGDKIKTQEFPQILTLIGRNPVGYPLAWQFLRKNWNKLVQKFELGSSSIAHMVMGTTNQFSTRTRLEEVKGFFSSLKENGSQLRCVQQTIETIEENIG` `________________________________________________________________________________________________________________________` `____________________` `3mdj(A) : WMDKNFDKIRVWLQ******` `:` `2yd0(A) : WMDKNFDKIRVWLQSEKLER` `____________________`

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)	14.0
Translation (A)	-0.5
Closure (%)	72.9
Bending Residues ( green )	395 - 407 412 - 440 517 - 518 522 - 527
Bending Region Analysis

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( yellow )	3
Rotation Angle (deg)	21.0
Translation (A)	-0.8
Closure (%)	69.6
Bending Residues ( green )	646 - 655 678 - 679
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: Mixed

PyMOL Script

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