SMTL ID : 2i5j.1

Crystal structure of HIV-1 reverse transcriptase (RT) in complex with DHBNH, an RNASE H inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.15 Å

Oligo State

hetero-1-1-mer

Ligands

2 x GLC- FRU: beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose(Non-covalent)

GLC-FRU.1: 6 residues within 4Å: Chain A: Q.340, Y.342, E.344, P.345, F.346, N.348 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.344, A:F.346, A:N.348 GLC-FRU.2: 9 residues within 4Å: Chain B: V.21, W.24, D.76, R.78, E.79, K.82, E.399, E.413, W.414 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:W.24, B:R.78, B:E.399, B:W.414, B:E.79, B:E.79, B:K.82, B:K.82, B:W.414, B:W.414

3 x GLC: alpha-D-glucopyranose(Non-covalent)

GLC.3: 6 residues within 4Å: Chain A: G.112, A.114, Y.115, F.116, Q.151, D.185 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.112, A:A.114, A:Y.115, A:Q.151, A:D.185 GLC.4: 4 residues within 4Å: Chain A: M.230, G.231, G.262, W.266 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.230, A:M.230, A:G.262 GLC.7: 3 residues within 4Å: Chain B: Y.354, E.370, Q.407 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.354, B:Q.407

1 x K05: (E)-3,4-DIHYDROXY-N'-[(2-METHOXYNAPHTHALEN-1-YL)METHYLENE]BENZOHYDRAZIDE(Non-covalent)

K05.5: 9 residues within 4Å: Chain A: V.108, D.186, L.187, Y.188, K.223, P.226, F.227, L.228, W.229 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:V.108, A:Y.188, A:K.223, A:L.228, A:L.228, A:L.228, A:W.229 Hydrogen bonds: A:D.186, A:L.228, A:L.228, A:W.229

1 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 3 residues within 4Å: Chain A: D.443, D.498, D.549 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.443, A:D.498

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Himmel, D.M. et al., HIV-1 reverse transcriptase structure with RNase H inhibitor dihydroxy benzoyl naphthyl hydrazone bound at a novel site. Acs Chem.Biol. (2006)

Release Date

2006-12-05

Peptides

Reverse transcriptase/ribonuclease H P66 subunit: A
Reverse transcriptase/ribonuclease H P51 subunit: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Reverse transcriptase/ribonuclease H P66 subunit

Reverse transcriptase/ribonuclease H P51 subunit

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