SMTL ID : 5hlf.1 (1 other biounit)

STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE In COMPLEX WITH A 38-MER HAIRPIN TEMPLATE-PRIMER DNA APTAMER AND AN ALPHA-CARBOXYPHOSPHONATE INHIBITOR

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.95 Å

Oligo State

hetero-1-1-mer

Ligands

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

GLC-FRU.1: 11 residues within 4Å: Chain B: V.37, D.92, R.94, E.95, K.98, K.411, E.415, E.429, W.430, F.432 Ligands: GOL.8 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.411, B:W.430, B:D.92, B:E.95, B:K.98, B:K.98, B:W.430, B:W.430

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.110, V.111, D.185 Ligands: 64A.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:V.111, A:D.185 MG.4: 3 residues within 4Å: Chain A: D.443, D.498, D.549 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.443, A:D.443, A:D.549, H2O.1

1 x 64A: {[(1S,3R)-3-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)cyclopentyl]oxy}propanedioic acid(Non-covalent)

64A.3: 12 residues within 4Å: Chain A: R.72, V.111, D.113, A.114, Y.115, Q.151, M.184, D.185 Chain C: A.5, C.6, G.38 Ligands: MG.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.115 Hydrogen bonds: A:D.113, A:A.114, A:Y.115 Salt bridges: A:R.72, A:R.72

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 3 residues within 4Å: Chain A: K.331, G.333, Q.334 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.334 Salt bridges: A:K.331

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 8 residues within 4Å: Chain A: L.503, Q.507, Y.532, L.533, A.534, W.535 Chain B: K.275, L.438 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.275, B:L.438 GOL.7: 6 residues within 4Å: Chain B: G.332, V.333, Y.334, K.339, Q.359, E.360 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.334, B:Y.334, B:Q.359 GOL.8: 5 residues within 4Å: Chain B: W.40, E.415, W.418, W.430 Ligands: GLC-FRU.1 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.94, B:E.415 GOL.9: 8 residues within 4Å: Chain A: L.92, G.93, V.381 Chain B: Q.39, W.40, P.41, P.149, N.153 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:L.92, B:Q.39, B:N.153 GOL.10: 10 residues within 4Å: Chain A: K.366, T.369, Q.373, W.401, Q.407, A.408, T.409 Chain B: I.409, Q.410, T.413 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.373, A:W.401, A:Q.407, A:A.408, A:T.409, B:Q.410 GOL.11: 7 residues within 4Å: Chain B: I.79, K.80, K.81, T.419, E.420, W.422, Q.423 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.80, B:W.422, B:Q.423

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mullins, N.D. et al., Exploring the role of the alpha-carboxyphosphonate moiety in the HIV-RT activity of alpha-carboxy nucleoside phosphonates. Org.Biomol.Chem. (2016)

Release Date

2016-02-10

Peptides

HIV-1 REVERSE TRANSCRIPTASE P66 SUBUNIT: A
HIV-1 REVERSE TRANSCRIPTASE P51 SUBUNIT: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

HIV-1 REVERSE TRANSCRIPTASE P66 SUBUNIT

HIV-1 REVERSE TRANSCRIPTASE P51 SUBUNIT

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