3HYF: Reverse transcriptase/RNaseH

Crystal structure of HIV-1 RNase H p15 with engineered E. coli loop and active site inhibitor. Determined by X-ray diffraction at 1.7 Å resolution. Released 20 Oct 2009.

Method: X-ray diffraction
Resolution: 1.7 Å
Organisms: Human immunodeficiency virus 1, Escherichia coli
Chains: 1
Atoms: 1,370
Mol. weight: 17.59 kDa
Ligands: MN, ON1
Released: 20 Oct 2009

Explore 3HYF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3HYF contains 5 α-helices and 5 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	433-434	2
β-strand	438-446	9	1
β-strand	453-459	7	1
β-strand	464-469	6	1
α-helix	474-488	15
β-strand	492-497	6	1
α-helix	500-87	16
α-helix	101-525	11
β-strand	530-535	6	1
α-helix	543-553	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Reverse transcriptase/RNaseH	A	protein	150	Human immunodeficiency virus 1, Escherichia coli	P0A7Y4 (AlphaFold model), Q72547

Sequence of entity 1 (A), FASTA

>3HYF_1 Reverse transcriptase/RNaseH (chains A)
MYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLA
LQDSGLEVNIVTDSQYALGIITQWIHNWKKRGWKTADKKPVKNVDLVNQIIEQLIKKEKV
YLAWVPAHKGIGGNEQVDKLVSAGIRKVLF

Ligands and cofactors

ID	Name	Formula	Copies
MN	Manganese (II) ion	Mn	2
ON1	2-(3,4-dichlorobenzyl)-5,6-dihydroxypyrimidine-4-carboxylic acid	C12 H8 Cl2 N2 O4	1

Water and common crystallization additives (ACT, GOL) are not listed.

Primary citation

RNase H active site inhibitors of human immunodeficiency virus type 1 reverse transcriptase: design, biochemical activity, and structural information. Kirschberg, T.A., Balakrishnan, M., Squires, N.H. et al. J Med Chem (2009) 52:5781-5784. DOI 10.1021/jm900597q · PubMed

Other PDB entries of the same protein (UniProt P0A7Y4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1JL1 1.3 Å, D10A E. coli ribonuclease HI
1F21 1.4 Å, Divalent metal cofactor binding in the kinetic folding trajectory of E. Coli…
2YV0 1.4 Å, Structural and Thermodynamic Analyses of E. coli ribonuclease HI Variant with Quintuple…
3QIO 1.4 Å, Crystal Structure of HIV-1 RNase H with engineered E. coli loop and N-hydroxy…
2RN2 1.48 Å, Structural details of ribonuclease H from escherichia coli as refined to an atomic…
1JXB 1.6 Å, I53A, a point mutant of the cysteine-free variant of E. coli Rnase HI
3QIN 1.7 Å, Crystal Structure of HIV-1 RNase H p15 with engineered E. coli loop and pyrimidinol…
7VSD 1.7 Å, E. coli Ribonuclease HI in complex with one Mg2+ (2)
1JL2 1.76 Å, Crystal structure of TCEO RNase H-a chimera combining the folding core from T.…
7VSA 1.76 Å, E. coli Ribonuclease HI in complex with two Mg2+
3AA4 1.79 Å, A52V E.coli RNase HI
1KVA 1.8 Å, E. Coli ribonuclease hi D134A mutant

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