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) 		1vrt (A)
  Conformer 2
(PDB) 		1ep4 (A)
  Window Length 5
  Minimum ratio 1.0
  Minimum domain size 20

Domains

Domain Size Backbone RMSD
(A)		 Residues
1 130 0.91   231 - 244   313 - 426   511 - 512
2 198 1.26   6 - 214
3 66 0.62   245 - 311
4 98 0.56   427 - 510   513 - 537

Sequence


           ________________________________________________________________________________________________________________________ 
 1vrt(A) : PIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDED 
         :                                                                                                                          
 1ep4(A) : PIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIK------wRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDED 
           ________________________________________________________________________________________________________________________ 

           _______________________________________________________________________________________213_________________________241__ 
 1vrt(A) : FRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQP 
         :                                                                                                                          
 1ep4(A) : FRKYTAFTIPSIN-----iRYQYNVLPQGWKGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLTTPD--hQKEPPFLWMGYELHPDKWTVQP 
           _______________________________________________________________________________________213_________________________241__ 

           _________________________________________________________________311____________________________________________________ 
 1vrt(A) : IVLPEKDSWTVNDIQKLVGKLNWASQIYPGIKVRQLCKLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTN 
         :                                                                                                                          
 1ep4(A) : IVLPEKDSWTVNDIQKLVGKLNWASQIYPGIKVRQL-kLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTN 
           _________________________________________________________________311____________________________________________________ 

           ____________________________________________________________426_________________________________________________________ 
 1vrt(A) : DVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVD-----------aGYVTNRGRQKVVTLTDTTNQKTELQAIY 
         :                                                                                                                          
 1ep4(A) : DVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIY 
           ____________________________________________________________426_________________________________________________________ 

           ________________________510_____________________________                                                                 
 1vrt(A) : LALQDSGLEVNIVTDSQYALGIIQAQPDQSESELVNQIIEQLIKKEKVYLAWVPAH                                                                 
         :                                                                                                                          
 1ep4(A) : LALQDSGLEVNIVTDSQYALGIIQAQPDQSESELVNQIIEQLIKKEKVYLAWVPAH                                                                 
           ________________________510_____________________________                                                                 

Morph

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Domain Pairs

Property Value
Fixed Domain
( blue ) 		1
Moving Domain
( red ) 		2
Rotation Angle
(deg) 		12.7
Translation
(A) 		-0.6
Closure
(%) 		4.5
Bending Residues
( green ) 		  213 - 231
Bending Region Analysis
Property Value
Fixed Domain
( blue ) 		1
Moving Domain
( yellow ) 		3
Rotation Angle
(deg) 		14.6
Translation
(A) 		4.2
Closure
(%) 		71.2
Bending Residues
( green ) 		  241 - 246
  311 - 317
Bending Region Analysis
Property Value
Fixed Domain
( blue ) 		1
Moving Domain
( violet ) 		4
Rotation Angle
(deg) 		13.6
Translation
(A) 		0.0
Closure
(%) 		31.1
Bending Residues
( green ) 		  426 - 427
  510 - 513
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

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

Conformer 2 Contact:
Residue 4 ———› Residue 1

Movement classification: Mixed

PyMOL Script

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