6WB2A

+3 extended hiv-1 reverse transcriptase initiation complex core (displaced state)
Total Genus 87
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The genus trace: a function that shows values of genus (vertical axis) for subchains spanned between the first residue, and all other residues (shown on horizontal axis). The number of the latter residue and the genus of a given subchain are shown interactively.

Total Genus
87
sequence length
556
structure length
540
Chain Sequence
SPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFKKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLTTPPFLWMGYELHPDKWTVQPIVLPEKDSWTVNDICKLVGKLNWASQIYPGIKVRQLSKLLRGTKALTEVIPTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNKGRQKVVPLTNTTNQKTQLQAIYLALQDSGLEVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIRK
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The genus matrix. At position (x,y) a genus value for a subchain spanned between x’th and y’th residue is shown. Values of the genus are represented by color, according to the scale given on the right.

Structure visualization

After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.

Chord Diagram
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publication title Distinct Conformational States Underlie Pausing during Initiation of HIV-1 Reverse Transcription.
pubmed doi rcsb
source organism Human immunodeficiency virus 1
molecule tags Viral protein/rna
molecule keywords HIV-1 viral RNA genome fragment
total genus 87
structure length 540
sequence length 556
ec nomenclature ec 2.7.7.49: RNA-directed DNA polymerase.
pdb deposition date 2020-03-26

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF00075 RNase_H RNase H
A PF00078 RVT_1 Reverse transcriptase (RNA-dependent DNA polymerase)
A PF06815 RVT_connect Reverse transcriptase connection domain
A PF06817 RVT_thumb Reverse transcriptase thumb domain
Image from the rcsb pdb (www.rcsb.org)
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similar chains in the Genus database (?% sequence similarity)
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similar chains in the pdb database (?% sequence similarity)

 
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