Human Immunodeficiency Virus Type 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 Human Immunodeficiency Virus Type 1 Reverse Transcriptase
  Conformer 1
(PDB) 		1dlo (A)
  Conformer 2
(PDB) 		1dlo (B)
  Window Length 5
  Minimum ratio 1.0
  Minimum domain size 20

Domains

Domain Size Backbone RMSD
(A)		 Residues
1 74 1.88   97 - 114   161 - 216
2 133 1.61   3 - 89   115 - 160
3 76 2.41   240 - 315
4 104 2.92   316 - 419

Sequence


           _______________________________________________________________________________________89______________________114______ 
 1dlo(A) : PISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPL 
         :                                                                                                                          
 1dlo(B) : PISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPL 
           _______________________________________________________________________________________89______________________114______ 

           _____________________________________160_____________________________________________________216________________________ 
 1dlo(A) : DEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFKKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWT 
         :                                                                                                                          
 1dlo(B) : DEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFKKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLTTPD------------gYELHPDKWT 
           _____________________________________160_____________________________________________________216________________________ 

           ________________________________________________________________________315_____________________________________________ 
 1dlo(A) : VQPIVLPEKDSWTVNDIQKLVGKLNWASQIYPGIKVRQLSKLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGA 
         :                                                                                                                          
 1dlo(B) : VQPIVLPEKDSWTVNDIQKLVGKLNWASQIYPGIKVRQLSKLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGA 
           ________________________________________________________________________315_____________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1dlo(A) : HTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNKGRQKVVPLTNTTNQKTELQ 
         :                                                                                                                          
 1dlo(B) : HTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEYWQATWIPEWEFVNTPPLVKLWY***************************************************** 
           ________________________________________________________________________________________________________________________ 

           ____________________________________________________________________________                                             
 1dlo(A) : AIYLALQDSGLEVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGI                                             
         :                                                                                                                          
 1dlo(B) : ****************************************************************************                                             
           ____________________________________________________________________________                                             

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Domain Pairs

Fixed Domain Moving Domain Rotation Angle Translation   (A) Closure Bending Residues  
1 2 54.9 0.0 85.4   89 - 103   114 - 115   160 - 161 Bending Region Analysis
1 3 110.1 -6.7 90.7   216 - 242 Bending Region Analysis
4 3 156.5 -4.8 40.5   315 - 318 Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification: Hinge

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:

No Contacts

PyMOL Script

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