DynDom - Protein Domain Motions

Hiv-1 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	Hiv-1 Reverse Transcriptase
Conformer 1 (PDB)	1ep4 (A)
Conformer 2 (PDB)	1rtj (A)
Window Length	9
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	325	2.46	88 - 102 225 - 535
2	175	1.42	22 - 87 103 - 224

Sequence

`_____________________________________________________________________________________87____________102__________________` `1ep4(A) : *PIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIK------wRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPL` `:` `1rtj(A) : PISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPL` `_____________________________________________________________________________________87____________102__________________` `_______________________________________________________________________________________________218______________________` `1ep4(A) : DEDFRKYTAFTIPSIN-----iRYQYNVLPQGWKGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLTTPD--hQKEPPFLWMGYELHPDKWT` `:` `1rtj(A) : DEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWT` `_______________________________________________________________________________________________218______________________` `________________________________________________________________________________________________________________________` `1ep4(A) : VQPIVLPEKDSWTVNDIQKLVGKLNWASQIYPGIKVRQL-kLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGA` `:` `1rtj(A) : VQPIVLPEKDSWTVNDIQKLVGKLNWASQIYPGIKVRQLCKLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGA` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1ep4(A) : HTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQ` `:` `1rtj(A) : HTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQ` `________________________________________________________________________________________________________________________` `_______________________________________________________________` `1ep4(A) : AIYLALQDSGLEVNIVTDSQYALGIIQAQPDQSESELVNQIIEQLIKKEKVYLAWVPAH**` `:` `1rtj(A) : AIYLALQDSGLEVNIVTDSQYALGIIQAQPDQSESELVNQIIEQLIKKEKVYLAWVPAHKGIG` `_______________________________________________________________`

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)	10.2
Translation (A)	-1.0
Closure (%)	56.0
Bending Residues ( green )	87 - 88 102 - 106 218 - 234
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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