DynDom - Protein Domain Motions

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	Reverse Transcriptase
Conformer 1 (PDB)	1j5o (A)
Conformer 2 (PDB)	1rtd (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	445	1.35	3 - 11 89 - 123 148 - 148 153 - 552
2	105	1.96	12 - 88 124 - 147 149 - 152

Sequence

`_________11___________________________________________________________________________88________________________________` `1j5o(A) : PISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPL` `:` `1rtd(A) : KISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPL` `_________11___________________________________________________________________________88________________________________` `123_____________________147__152________________________________________________________________________________________` `1j5o(A) : DEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFKKQNPDIVIYQYIDDLYVGSDLEIGQHRTKIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWT` `:` `1rtd(A) : DEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWT` `123_____________________147__152________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1j5o(A) : VQPIVLPEKDSWTVNDIQKLVGKLNWASQIYPGIKVRQLSKLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGA` `:` `1rtd(A) : VQPIVLPEKDSWTVNDICKLVGKLNWASQIYPGIKVRQLCKLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGA` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1j5o(A) : HTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNKGRQKVVPLTNTTNQKTELQ` `:` `1rtd(A) : HTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNKGRQKVVPLTDTTNQKTQLQ` `________________________________________________________________________________________________________________________` `______________________________________________________________________________` `1j5o(A) : AIYLALQDSGLEVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIRK` `:` `1rtd(A) : AIYLALQDSGLEVNIVTDSQYALGIIQAQPDESESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSA****` `______________________________________________________________________________`

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)	14.8
Translation (A)	0.6
Closure (%)	97.5
Bending Residues ( green )	11 - 12 88 - 89 123 - 124 147 - 149 152 - 153
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification: Shear

PyMOL Script

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