SMTL ID : 8jyi.1

Crystal structure of engineered HIV-1 Reverse Transcriptase RNase H domain complexed with laccaic acid E

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

monomer

Ligands

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 6 residues within 4Å: Chain A: D.23, G.24, E.58, D.78 Ligands: MN.2, V9O.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.23, A:E.58, A:D.78, A:D.78 MN.2: 6 residues within 4Å: Chain A: D.23, D.78, D.139, R.147 Ligands: MN.1, V9O.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.23, A:D.78, A:D.139

1 x V9O: 7-[5-(2-azanylethyl)-2-oxidanyl-phenyl]-3,5,6,8-tetrakis(oxidanyl)-9,10-bis(oxidanylidene)anthracene-1,2-dicarboxylic acid(Non-covalent)

V9O.3: 11 residues within 4Å: Chain A: D.23, E.58, D.78, S.79, Q.80, Y.81, A.128, D.139, R.147 Ligands: MN.1, MN.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.128 Hydrogen bonds: A:Q.80, A:Y.81, A:R.147, A:R.147

2 x ZN: ZINC ION(Non-covalent)

ZN.4: 3 residues within 4Å: Chain A: H.129, G.133, E.136 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.129, A:E.136, A:E.136 ZN.5: 2 residues within 4Å: Chain A: E.72, E.119 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.72, A:E.119, A:E.119, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ito, Y. et al., Sticklac-Derived Natural Compounds Inhibiting RNase H Activity of HIV-1 Reverse Transcriptase. J.Nat.Prod. (2023)

Release Date

2023-08-16

Peptides

Pol protein,Pol protein,Ribonuclease H: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Pol protein,Pol protein,Ribonuclease H

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