DynDom - Protein Domain Motions

Hiv-1 Reverse Transcriptase (Subunit P66)

(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 (Subunit P66)
Conformer 1 (PDB)	1hmv (A)
Conformer 2 (PDB)	1fk9 (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	415	2.82	6 - 223 229 - 232 316 - 537
2	87	1.79	224 - 228 233 - 315

Sequence

`________________________________________________________________________________________________________________________` `1hmv(A) : PISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAI------vDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDEDFR` `:` `1fk9(A) : *PIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAItKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDEDFR` `________________________________________________________________________________________________________________________` `_________________________________________________________________________________________217________228_________________` `1hmv(A) : KYTAFTIP-------gIRYQYNVLPQGWKGSPAIFQSSMTKILEPFKKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIV` `:` `1fk9(A) : KYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIV` `_________________________________________________________________________________________217________228_________________` `__________________________________________________________________314___________________________________________________` `1hmv(A) : LPEKDSWTVNDIQKLVGKLNWASQIYPGIKVRQLCKLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDV` `:` `1fk9(A) : LPEKDSWTVNDIQKLVGKLNWASQIYPGIKVRQL-kLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDV` `__________________________________________________________________314___________________________________________________` `________________________________________________________________________________________________________________________` `1hmv(A) : KQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNKGRQKVVPLTNTTNQKTELQAIYLA` `:` `1fk9(A) : KQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVD-----------aGYVTNRGRQKVVTLTDTTNQKTELQAIYLA` `________________________________________________________________________________________________________________________` `_____________________________________________________________________` `1hmv(A) : LQDSGLEVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSA` `:` `1fk9(A) : LQDSGLEVNIVTDSQYALGIIQAQPDQSESELVNQIIEQLIKKEKVYLAWVPAH*************` `_____________________________________________________________________`

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)	41.3
Translation (A)	0.0
Closure (%)	4.0
Bending Residues ( green )	217 - 224 228 - 229 231 - 233 314 - 316
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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