Brand  (β version)

PDB ID: 5HBM

Hetero Atom Contents

  The number of atoms exceeds 100,000.
  So, it can not be displayed here.

Select unit:

Select hetatm:   

close
information
centroid:
interaction residue:

Select chain:   Sequence  

Data format:   

Color scheme of protein:

Ligands
Code Name Style Show Link
F95 (7,8-dihydroxy-2-oxo-2h-chromen-4-yl)acetic acid PoSSuM
MN Manganese (II) ion PoSSuM
NVP 11-cyclopropyl-5,11-dihydro-4-methyl-6h-dipyrido[3,2-B:2',3'-E][1,4]diazepin-6-one PoSSuM
Non-standard Residues
Code Name Show
Glycosylation
Code Name Emphasize
Modification
Code Name Show

Structure summary

Code : 5HBM   PDBj   RCSB PDB   PDBe
Header : TRANSFERASE, HYDROLASE/INHIBITOR
Title : Crystal Structure of a Dihydroxycoumarin RNase H Active-Site Inhibitor in Complex with HIV-1 Reverse Transcriptase
Release Data : 2016-02-24
Compound :
mol_id molecule chains synonym
1 Reverse transcriptase/ribonuclease H A Exoribonuclease H, p66 RT
ec: 2.7.7.49,2.7.7.7,3.1.26.13,3.1.13.2
fragment: p66 domain, residues 600-1153
mutation: K172A, K173A, C280S
mol_id molecule chains synonym
2 p51 RT B Pr160Gag-Pol
fragment: p51 domain, residues 604-1027
mutation: C280S
Source :
mol_id organism_scientific organism_common expression_system
1 Human immunodeficiency virus type 1 BH10  (taxid:11678) HIV-1 Escherichia coli  (taxid:469008)
strain: isolate BH10
gene: gag-pol
expression_system_strain: BL21 (DE3) RIL
expression_system_vector_type: plasmid
expression_system_plasmid: pET52a
mol_id organism_scientific organism_common expression_system
2 Human immunodeficiency virus type 1 BH10  (taxid:11678) HIV-1 Escherichia coli  (taxid:469008)
strain: isolate BH10
gene: gag-pol
expression_system_strain: BL21 (DE3) RIL
expression_system_vector_type: plasmid
expression_system_plasmid: pET52a
Authors : Kirby, K.A., Sarafianos, S.G.
Keywords : TRANSFERASE, HYDROLASE, INHIBITOR, HYDROLASE-INHIBITOR complex
Exp. method : X-RAY DIFFRACTION ( 3.0430 Å )
Citation :

Crystal Structure of a Dihydroxycoumarin RNase H Active-Site Inhibitor in Complex with HIV-1 Reverse Transcriptase

Kirby, K.A.,Sarafianos, S.G.
To Be Published 

Reaction

Chain : B
UniProt : P03366 (POL_HV1B1)
Reaction: EC: Evidence:
Physiological Direction:
Specific for a P1 residue that is hydrophobic, and P1' variable, but often Pro. 3.4.23.16 PROSITE-ProRule:PRU00275
-
3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid. 3.1.13.2 ECO:0000250
-
[Reverse transcriptase/ribonuclease H]
Endohydrolysis of RNA in RNA/DNA hybrids. Three different cleavage modes: 1. sequence-specific internal cleavage of RNA. Human immunodeficiency virus type 1 and Moloney murine leukemia virus enzymes prefer to cleave the RNA strand one nucleotide away from the RNA-DNA junction. 2. RNA 5'-end directed cleavage 13-19 nucleotides from the RNA end. 3. DNA 3'-end directed cleavage 15-20 nucleotides away from the primer terminus. 		3.1.26.13 PubMed:2476069
-
[Reverse transcriptase/ribonuclease H]
a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = diphosphate + DNA(n+1) 		2.7.7.49 PROSITE- ProRule:PRU00405, PubMed:2476069
-
[Reverse transcriptase/ribonuclease H]
a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = diphosphate + DNA(n+1) 		2.7.7.7 PROSITE- ProRule:PRU00405, PubMed:2476069
-