SMTL ID : 3hyf.1

Crystal structure of HIV-1 RNase H p15 with engineered E. coli loop and active site inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: D.18, E.53, D.73 Ligands: MN.2, ON1.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.18, A:E.53, A:D.73 MN.2: 4 residues within 4Å: Chain A: D.18, D.138 Ligands: MN.1, ON1.6 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.18, A:D.138, H2O.7, H2O.7

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 4 residues within 4Å: Chain A: Y.16, N.35, G.133, Q.136 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.16, A:N.35 Hydrogen bonds: A:Q.136 Water bridges: A:T.34, A:T.34, A:G.132

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 2 residues within 4Å: Chain A: R.36, G.65 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.36, A:R.36 Water bridges: A:E.13, A:G.65, A:G.65, A:L.66, A:L.66 GOL.5: 3 residues within 4Å: Chain A: T.48, N.49, Q.50 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.49, A:N.49, A:Q.50 Water bridges: A:N.22, A:N.49

1 x ON1: 2-(3,4-dichlorobenzyl)-5,6-dihydroxypyrimidine-4-carboxylic acid(Non-covalent)

ON1.6: 12 residues within 4Å: Chain A: D.18, E.53, D.73, S.74, A.127, H.128, K.129, D.138, R.146, L.149 Ligands: MN.1, MN.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.146 Water bridges: A:Q.75, A:Q.75 pi-Cation interactions: A:H.128

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kirschberg, T.A. et al., RNase H active site inhibitors of human immunodeficiency virus type 1 reverse transcriptase: design, biochemical activity, and structural information. J.Med.Chem. (2009)

Release Date

2009-10-20

Peptides

Reverse transcriptase/RNaseH: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Reverse transcriptase/RNaseH

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