SMTL ID : 6bsj.1

Structure of HIV-1 RT complexed with an RNA/DNA hybrid sequence non-preferred for RNA hydrolysis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.89 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 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.101, A:Y.182, A:Y.189, A:Y.189, A:W.230, A:L.235, A:Y.319 Hydrogen bonds: A:K.102, A:K.102, A:K.104

1 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: D.444, G.445, E.479, D.499 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.444, A:E.479, A:D.499

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: K.21, V.22, K.23, P.56, Y.57, N.58 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.57 GOL.4: 4 residues within 4Å: Chain A: P.5, I.6, E.7, W.213 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.7 GOL.5: 3 residues within 4Å: Chain C: T.17, G.18 Ligands: GOL.6 No protein-ligand interaction detected (PLIP) GOL.6: 3 residues within 4Å: Chain C: G.20, G.21 Ligands: GOL.5 No protein-ligand interaction detected (PLIP)

1 x TAM: TRIS(HYDROXYETHYL)AMINOMETHANE(Non-functional Binders)

TAM.7: 4 residues within 4Å: Chain C: G.5 Chain D: G.20, G.21, C.22 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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