3QIN: PDB entry 3QIN

Crystal Structure of HIV-1 RNase H p15 with engineered E. coli loop and pyrimidinol carboxylic acid inhibitor. Determined by X-ray diffraction at 1.7 Å resolution. Released 20 Apr 2011.

Method: X-ray diffraction
Resolution: 1.7 Å
Organisms: Human immunodeficiency virus type 1 group M subtype B, Escherichia coli (strain K12), Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)
Chains: 1
Atoms: 1,263
Mol. weight: 17.48 kDa
Ligands: MN, P1Y
Released: 20 Apr 2011

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

Secondary structure: helices and β-sheets

3QIN contains 4 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: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	439-446	8	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	500-85	14
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
Fusion protein of HIV-1 RNase H p15 with engineered E. coli loop	A	protein	150	Human immunodeficiency virus type 1 group M subtype B, Escherichia coli (strain K12), Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)	P04585 (AlphaFold model), P0A7Y4 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3QIN_1 Fusion protein of HIV-1 RNase H p15 with engineered E. coli loop (chains A)
MYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLA
LQDSGLEVNIVTDSQYALGIITQWIHNWKKRGWKTADKKPVKNVDLVNQIIEQLIKKEKV
YLAWVPAHKGIGGNEQVDKLVSAGIRKVLF

Ligands and cofactors

ID	Name	Formula	Copies
MN	Manganese (II) ion	Mn	2
P1Y	2-(3-bromo-4-methoxybenzyl)-5,6-dihydroxypyrimidine-4-carboxylic acid	C13 H11 Br N2 O5	1

Water and common crystallization additives (SO4) are not listed.

Primary citation

Structural and Binding Analysis of Pyrimidinol Carboxylic Acid and N-Hydroxy Quinazolinedione HIV-1 RNase H Inhibitors. Lansdon, E.B., Liu, Q., Leavitt, S.A. et al. Antimicrob Agents Chemother (2011) 55:2905-2915. DOI 10.1128/AAC.01594-10 · PubMed

Other PDB entries of the same protein (UniProt P04585 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6DV4 1.14 Å, HIV-1 wild type protease with GRL-04315A, a tetrahydronaphthalene carboxamide with…
6DIF 1.2 Å, Wild-type HIV-1 protease in complex with tipranavir
6DV0 1.2 Å, HIV-1 wild type protease with GRL-02815A, a thiochroman heterocycle with (S)-Boc-amine…
5DGU 1.22 Å, Crystal Structure of HIV-1 Protease Inhibitors Containing Substituted…
6E9A 1.22 Å, HIV-1 wild type protease with grl-034-17A, (3aS, 5R, 6aR)-2-oxohexahyd…
6DJ1 1.26 Å, Wild-type HIV-1 protease in complex with Lopinavir
8F0F 1.29 Å, HIV-1 wild type protease with GRL-110-19A, a chloroacetamide derivative based on…
6E7J 1.3 Å, HIV-1 wild type protease with GRL-042-17A, 3-phenylhexahydro-2h-cyclopenta[d]oxazol-2-one…
6DJ7 1.31 Å, HIV-1 protease with mutation L76V in complex with GRL-5010…
8ESX 1.35 Å, HIV protease in complex with benzoxaborolone analog of darunavir
8ESY 1.35 Å, D30N mutant HIV protease in complex with benzoxaborolone analog of darunavir
6DJ2 1.36 Å, HIV-1 protease with single mutation L76V in complex with Lopinavir

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