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

Structure of HIV-1 reverse transcriptase in complex with an RNase H inhibitor and nevirapine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

hetero-2-2-mer

Ligands

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.1: 14 residues within 4Å: Chain A: L.100, K.101, K.103, V.106, V.179, Y.181, Y.188, G.190, F.227, W.229, L.234, H.235, P.236, Y.318 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.106, A:V.179, A:Y.181, A:W.229, A:Y.318 NVP.9: 14 residues within 4Å: Chain C: L.100, K.101, K.103, V.106, V.179, Y.181, Y.188, G.190, F.227, W.229, L.234, H.235, P.236, Y.318 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:V.106, C:V.179, C:Y.181, C:W.229, C:Y.318

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

MN.2: 5 residues within 4Å: Chain A: D.443, E.478, D.498 Ligands: MN.3, P4Y.7 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.443, A:E.478, A:D.498 MN.3: 4 residues within 4Å: Chain A: D.443, D.549 Ligands: MN.2, P4Y.7 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.443, A:D.549, H2O.1, H2O.1 MN.10: 5 residues within 4Å: Chain C: D.443, E.478, D.498 Ligands: MN.11, P4Y.15 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.443, C:E.478, C:D.498 MN.11: 4 residues within 4Å: Chain C: D.443, D.549 Ligands: MN.10, P4Y.15 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.443, C:D.549, H2O.17, H2O.17

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

SO4.4: 6 residues within 4Å: Chain A: G.436, A.437, E.438, N.460, R.461 Chain B: A.288 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.460 Water bridges: A:T.439, A:T.439 Salt bridges: A:R.461 SO4.5: 3 residues within 4Å: Chain A: G.436, R.461, G.490 6 PLIP interactions: 6 interactions with chain A Water bridges: A:R.461, A:R.461, A:L.491, A:L.491, A:E.492 Salt bridges: A:R.461 SO4.12: 6 residues within 4Å: Chain C: G.436, A.437, E.438, N.460, R.461 Chain D: A.288 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.460 Water bridges: C:T.439, C:T.439 Salt bridges: C:R.461 SO4.13: 3 residues within 4Å: Chain C: G.436, R.461, G.490 6 PLIP interactions: 6 interactions with chain C Water bridges: C:R.461, C:R.461, C:L.491, C:L.491, C:E.492 Salt bridges: C:R.461

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 3 residues within 4Å: Chain A: S.515, E.516, L.517 Ligand excluded by PLIP CL.8: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain C: S.515, E.516, L.517 Ligand excluded by PLIP CL.16: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

2 x P4Y: 5,6-dihydroxy-2-[(2-phenyl-1H-indol-3-yl)methyl]pyrimidine-4-carboxylic acid(Non-covalent)

P4Y.7: 10 residues within 4Å: Chain A: D.443, E.478, D.498, A.538, H.539, D.549 Chain C: R.448 Ligands: MN.2, MN.3, P4Y.15 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.448 P4Y.15: 10 residues within 4Å: Chain A: R.448 Chain C: D.443, E.478, D.498, A.538, H.539, D.549 Ligands: P4Y.7, MN.10, MN.11 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.448

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lansdon, E.B. et al., Structural and Binding Analysis of Pyrimidinol Carboxylic Acid and N-Hydroxy Quinazolinedione HIV-1 RNase H Inhibitors. Antimicrob.Agents Chemother. (2011)

Release Date

2011-04-20

Peptides

Reverse HIV-1 reverse transcriptase p66: AC
p51: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

Reverse HIV-1 reverse transcriptase p66

p51

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