SMTL ID : 7lrx.1 (1 other biounit)

Structure of HIV-1 Reverse Transcriptase in complex with DNA, L-dCTP, and CA(2+) ion

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 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.22, W.25, D.77, R.79, E.80, K.83, K.396, E.400, E.414, W.415, F.417 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:D.77, B:K.396, B:W.415, B:D.77, B:E.80, B:E.80, B:K.83, B:K.83, B:W.415, B:W.415

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

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

1 x 1S0: 4-amino-1-{2-deoxy-5-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-L-erythro-pentofuranosyl}pyrimidin-2(1H)-one(Non-covalent)

1S0.3: 17 residues within 4Å: Chain A: K.65, K.70, R.72, D.110, V.111, G.112, D.113, A.114, Y.115, Q.151, M.184, D.185, K.220 Chain C: G.5, C.6, G.38 Ligands: CA.4 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:R.72, A:D.110, A:D.113, A:D.113, A:A.114, A:Y.115, A:Q.151 Salt bridges: A:K.65, A:K.65, A:K.65, A:K.70, A:R.72, A:K.220, A:K.220 pi-Cation interactions: A:R.72

1 x CA: CALCIUM ION(Non-covalent)

CA.4: 4 residues within 4Å: Chain A: D.110, V.111, D.185 Ligands: 1S0.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.110, A:D.110, A:V.111, A:D.185

1 x NH4: AMMONIUM ION(Non-functional Binders)

NH4.5: 3 residues within 4Å: Chain A: H.539, D.549, S.553 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.553, A:S.553

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 5 residues within 4Å: Chain B: G.317, V.318, Y.319, K.324, E.345 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.319, B:Y.319, B:K.324

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ruiz, F.X. et al., Structural basis of HIV inhibition by L-nucleosides: Opportunities for drug development and repurposing. Drug Discov Today (2022)

Release Date

2022-02-23

Peptides

Reverse transcriptase p66: A
Reverse transcriptase p51: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Reverse transcriptase p66

Reverse transcriptase p51

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