DynDom - Protein Domain Motions

Protein (Reverse Transcriptase)

(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	Protein (Reverse Transcriptase)
Conformer 1 (PDB)	1rtd (C)
Conformer 2 (PDB)	1fk9 (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	332	1.88	87 - 89 91 - 103 181 - 187 215 - 217 220 - 537
2	183	2.11	6 - 86 90 - 90 104 - 180 188 - 214 218 - 219

Sequence

`____________________________________________________________________________________86______________103_________________` `1rtd(C) : KISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPL` `:` `1fk9(A) : *PIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAI-----tKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPL` `____________________________________________________________________________________86______________103_________________` `_________________________________________________________180____187_______________________213_217_______________________` `1rtd(C) : DEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWT` `:` `1fk9(A) : DEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWT` `_________________________________________________________180____187_______________________213_217_______________________` `________________________________________________________________________________________________________________________` `1rtd(C) : VQPIVLPEKDSWTVNDICKLVGKLNWASQIYPGIKVRQLCKLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGA` `:` `1fk9(A) : VQPIVLPEKDSWTVNDIQKLVGKLNWASQIYPGIKVRQL-kLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGA` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1rtd(C) : HTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNKGRQKVVPLTDTTNQKTQLQ` `:` `1fk9(A) : HTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVD-----------aGYVTNRGRQKVVTLTDTTNQKTELQ` `________________________________________________________________________________________________________________________` `__________________________________________________________________________` `1rtd(C) : AIYLALQDSGLEVNIVTDSQYALGIIQAQPDESESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSA` `:` `1fk9(A) : AIYLALQDSGLEVNIVTDSQYALGIIQAQPDQSESELVNQIIEQLIKKEKVYLAWVPAH*************` `__________________________________________________________________________`

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)	24.2
Translation (A)	-1.6
Closure (%)	83.4
Bending Residues ( green )	86 - 96 103 - 104 180 - 181 187 - 188 213 - 215 217 - 229
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification: Hinge

PyMOL Script

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