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)	1sv5 (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	251	1.41	87 - 100 231 - 243 314 - 537
2	198	1.59	6 - 86 101 - 230
3	64	0.86	247 - 311

Sequence

`____________________________________________________________________________________86___________100____________________` `1ep4(A) : *PIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIK------wRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPL` `:` `1sv5(A) : PISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKNKSVTVLDVGDAYFSVPL` `____________________________________________________________________________________86___________100____________________` `___________________________________________________________________________________________________________230__________` `1ep4(A) : DEDFRKYTAFTIPSIN-----iRYQYNVLPQGWKGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLTTPD--hQKEPPFLWMGYELHPDKWT` `:` `1sv5(A) : DEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFKKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWT` `___________________________________________________________________________________________________________230__________` `243_________________________________________________________________311_________________________________________________` `1ep4(A) : VQPIVLPEKDSWTVNDIQKLVGKLNWASQIYPGIKVRQL-kLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGA` `:` `1sv5(A) : VQPIVLPEKDSWTVNDIQKLVGKLNWASQIYPGIKVRQLSKLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGA` `243_________________________________________________________________311_________________________________________________` `________________________________________________________________________________________________________________________` `1ep4(A) : HTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQ` `:` `1sv5(A) : HTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNKGRQKVVPLTNTTNQKTELQ` `________________________________________________________________________________________________________________________` `________________________________________________________________________` `1ep4(A) : AIYLALQDSGLEVNIVTDSQYALGIIQAQPDQSESELVNQIIEQLIKKEKVYLAWVPAH***********` `:` `1sv5(A) : AIYLALQDSGLEVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLV` `________________________________________________________________________`

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)	10.7
Translation (A)	-0.6
Closure (%)	89.5
Bending Residues ( green )	86 - 87 100 - 101 230 - 231
Bending Region Analysis

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( yellow )	3
Rotation Angle (deg)	26.5
Translation (A)	3.8
Closure (%)	68.3
Bending Residues ( green )	243 - 247 311 - 314
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification: Shear

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

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

Movement classification: Hinge

PyMOL Script

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