SMTL ID : 3lp1.2 (1 other biounit)

HIV-1 reverse transcriptase with inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.23 Å

Oligo State

hetero-2-2-mer

Ligands

2 x LP8: 3-cyclopentyl-1,4-dihydroxy-1,8-naphthyridin-2(1H)-one(Non-covalent)

LP8.1: 11 residues within 4Å: Chain A: D.446, G.447, E.481, D.501, A.541, H.542, D.552 Chain C: R.451 Ligands: MN.2, MN.3, LP8.5 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:A.541, C:R.451 LP8.5: 11 residues within 4Å: Chain A: R.451 Chain C: D.446, G.447, E.481, D.501, A.541, H.542, D.552 Ligands: LP8.1, MN.6, MN.7 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:A.541, A:R.451

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 4 residues within 4Å: Chain A: D.446, D.552 Ligands: LP8.1, MN.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.446, A:D.552, LP8.1 MN.3: 5 residues within 4Å: Chain A: D.446, E.481, D.501 Ligands: LP8.1, MN.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.446, A:E.481, A:D.501, LP8.1 MN.6: 4 residues within 4Å: Chain C: D.446, D.552 Ligands: LP8.5, MN.7 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:D.446, C:D.552, LP8.5 MN.7: 5 residues within 4Å: Chain C: D.446, E.481, D.501 Ligands: LP8.5, MN.6 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:D.446, C:E.481, C:D.501, LP8.5

2 x NVP: 11-CYCLOPROPYL-5,11-DIHYDRO-4-METHYL-6H-DIPYRIDO[3,2-B:2',3'-E][1,4]DIAZEPIN-6-ONE(Non-covalent)

NVP.4: 14 residues within 4Å: Chain A: L.103, K.104, N.106, V.109, V.182, Y.184, Y.191, G.193, F.230, W.232, L.237, H.238, P.239, Y.321 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.103, A:V.109, A:V.182, A:Y.184, A:Y.184, A:Y.191, A:Y.191, A:Y.191, A:W.232, A:L.237, A:Y.321 NVP.8: 14 residues within 4Å: Chain C: L.103, K.104, N.106, V.109, V.182, Y.184, Y.191, G.193, F.230, W.232, L.237, H.238, P.239, Y.321 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:L.103, C:V.109, C:V.182, C:Y.184, C:Y.184, C:Y.191, C:Y.191, C:Y.191, C:W.232, C:L.237, C:Y.321

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Su, H.P. et al., Structural basis for the inhibition of RNase H activity of HIV-1 reverse transcriptase by RNase H active site-directed inhibitors. J.Virol. (2010)

Release Date

2010-06-09

Peptides

Reverse transcriptase/ribonuclease H: AC
p51 RT: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

Reverse transcriptase/ribonuclease H

p51 RT

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