DynDom - Protein Domain Motions

Proaerolysin

(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	Proaerolysin
Conformer 1 (PDB)	1pre (A)
Conformer 2 (PDB)	3c0n (A)
Window Length	13
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	229	0.67	84 - 96 106 - 189 235 - 251 257 - 273 306 - 403
2	76	0.36	8 - 83
3	126	0.94	97 - 105 190 - 234 252 - 252 274 - 305 404 - 462

Sequence

`________________________________________________________________________________83___________96______105________________` `1pre(A) : EPVYPDQLRLFSLGQGVCGDKYRPVNREEAQSVKSNIVGMMGQWQISGLANGWVIMGPGYNGEIKPGTASNTWCYPTNPVTGEIPTLSALDIPDGDEVDVQWRLVHDSANFIKPTSYLAH` `:` `3c0n(A) : EPVYPDQLRLFSLGQGVCGDKYRPVNREEAQSVKSNIVGMMGQWQISGLANGWVIMGPGYNGEIKPGTASNTWCYPTNPVTGEIPTLSALDIPDGDEVDVQWRLVHDSANFIKPTSYLAH` `________________________________________________________________________________83___________96______105________________` `_________________________________________________________________189__________________________________________234_______` `1pre(A) : YLGYAWVGGNHSQYVGEDMDVTRDGDGWVIRGNNDGGCDGYRCGDKTAIKVSNFAYNLDPDSFKHGDVTQSDRQLVKTVVGWAVND---pQSGYDVTLRYDTATNWSKTNTYGLSEKVTT` `:` `3c0n(A) : YLGYAWVGGNHSQYVGEDMDVTRDGDGWVIRGNNDGGCDGYRCGDKTAIKVSNFAYNLDPDSFKHGDVTQSDRQLVKTVVGWAVNDSDTPQSGYDVTLRGDTATNWSKTNTYGLSEKVTT` `_________________________________________________________________189__________________________________________234_______` `___247_______________________273_____________________________305________________________________________________________` `1pre(A) : KNKFKWPLVGETELSIEIAANQSWASQNGGSTTTSLSQSVRPTVPARSKIPVKIELYKADISYPYEFKADVSYDLTLSGFLRWGGNAWYTHPDNRPNWNHTFVIGPYKDKASSIRYQWDK` `:` `3c0n(A) : KNKFKWPLVGETELSIEIAANQSWASQNGGSTTTSLSQSVRPTVPARSKIPVKIELYKADISYPYEFKADVSYDLTLSGFLRWGGNAWYTHPDNRPNWNHTFVIGPYKDKASSIRYQWDK` `___247_______________________273_____________________________305________________________________________________________` `_______________________________________403__________________________________________________` `1pre(A) : RYIPGEVKWWDWNWTIQQNGLSTMQNNLARVLRPVRAGITGDFSAESQFAGNIEIGAPVPLgLRLEIPLDAQELSGLGFNNVSLSVTPAANQ` `:` `3c0n(A) : RYIPGEVKWWDWNWTIQQNGLSTMQNNLARVLRPVRAGITGDFSAESQFAGNIEIGAPVPLgLRLEIPLDAQELSGLGFNNVSLSVTPAA**` `_______________________________________403__________________________________________________`

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)	7.0
Translation (A)	-0.5
Closure (%)	21.8
Bending Residues ( green )	83 - 85
Bending Region Analysis

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( yellow )	3
Rotation Angle (deg)	5.3
Translation (A)	0.5
Closure (%)	27.5
Bending Residues ( green )	96 - 97 105 - 106 189 - 190 234 - 235 247 - 259 273 - 274 305 - 306 403 - 404
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: Shear

PyMOL Script

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