DynDom - Protein Domain Motions

Reverse Transcriptase/ribonuclease H

(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/ribonuclease H
Conformer 1 (PDB)	3dle (A)
Conformer 2 (PDB)	3lak (B)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	72	1.94	97 - 114 161 - 214
2	128	1.79	7 - 91 115 - 160
3	83	4.81	215 - 233 235 - 315
4	101	3.63	234 - 234 316 - 419

Sequence

`_________________________________________________________________________________85__________________________114________` `3dle(A) : PISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIKK-tKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDE` `:` `3lak(B) : **IETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIKKsTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDE` `_________________________________________________________________________________85__________________________114________` `___________________________________160___________________________________________________214____________________________` `3dle(A) : DFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQ` `:` `3lak(B) : DFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLT----------------yELHPDKWTVQ` `___________________________________160___________________________________________________214____________________________` `_____________________________________________________________________314________________________________________________` `3dle(A) : PIVLPEKDSWTVNDIQKLVGKLNWASQIYPGIKVRQL-kLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHT` `:` `3lak(B) : PIVLPEKDSWTVNDIQKLVGKLNWASQIYPGIKVRQLCKLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYAR----hT` `_____________________________________________________________________314________________________________________________` `________________________________________________________________________________________________________________________` `3dle(A) : NDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAI` `:` `3lak(B) : NDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEYWQATWIPEWEFVNTPPLVKLWYQL*************************************************` `________________________________________________________________________________________________________________________` `________________________________________________________` `3dle(A) : YLALQDSGLEVNIVTDSQYALGIIQAQPDQSESELVNQIIEQLIKKEKVYLAWVPA` `:` `3lak(B) : ******************************************************` `________________________________________________________`

Morph

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Status: Initialising

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Domain Pairs

Fixed Domain	Moving Domain	Rotation Angle	Translation (A)	Closure	Bending Residues
1	2	49.3	-1.2	84.7	85 - 103 114 - 115 160 - 161	Bending Region Analysis
1	3	78.0	-2.0	53.8	214 - 233	Bending Region Analysis
4	3	116.6	-3.7	18.6	215 - 243 314 - 317	Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification: Hinge

Conformer 1 Contact:
Residue 4 ———› Residue 3

Conformer 2 Contact:
Residue 3 ———› Residue 4

Movement classification: Hinge

PyMOL Script

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