SMTL ID : 6bsg.1

Structure of HIV-1 RT complexed with RNA/DNA hybrid in an RNA hydrolysis-off mode

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.44 Å

Oligo State

hetero-1-1-mer

Ligands

1 x EFZ: (-)-6-CHLORO-4-CYCLOPROPYLETHYNYL-4-TRIFLUOROMETHYL-1,4-DIHYDRO-2H-3,1-BENZOXAZIN-2-ONE(Non-covalent)

EFZ.1: 14 residues within 4Å: Chain A: L.101, K.102, K.104, V.107, V.180, Y.182, Y.189, V.190, G.191, F.228, W.230, L.235, H.236, Y.319 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:K.104, A:Y.182, A:Y.189, A:Y.189, A:Y.189, A:W.230, A:W.230, A:L.235, A:Y.319 Hydrogen bonds: A:K.102, A:K.102

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain A: D.444, E.479, D.499 Chain D: C.22, A.23 Ligands: CA.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.444, A:E.479, A:D.499 CA.3: 6 residues within 4Å: Chain A: D.444, G.445, D.550, R.558 Chain D: A.23 Ligands: CA.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.444, A:D.550

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: K.21, V.22, K.23, P.56, Y.57, N.58, R.144 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.21, A:Y.57 GOL.5: 3 residues within 4Å: Chain B: N.266, S.269, Q.270 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.266 Water bridges: B:Q.270, B:Q.270 GOL.6: 6 residues within 4Å: Chain A: Q.86 Chain B: E.54, N.55, P.56, Y.57, K.127 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.57, B:K.127, B:K.127 Water bridges: A:D.87 GOL.7: 4 residues within 4Å: Chain C: T.17, G.18 Chain D: C.6, C.7 No protein-ligand interaction detected (PLIP)

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.8: 4 residues within 4Å: Chain C: C.6, C.7 Chain D: G.20, G.21 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tian, L. et al., Structure of HIV-1 reverse transcriptase cleaving RNA in an RNA/DNA hybrid. Proc. Natl. Acad. Sci. U.S.A. (2018)

Release Date

2018-01-03

Peptides

REVERSE TRANSCRIPTASE P66 SUBUNIT: A
REVERSE TRANSCRIPTASE P51 SUBUNIT: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

REVERSE TRANSCRIPTASE P66 SUBUNIT

REVERSE TRANSCRIPTASE P51 SUBUNIT

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