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

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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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