SMTL ID : 6avm.2 (1 other biounit)

STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE (RT) TERNARY COMPLEX WITH A DOUBLE STRANDED DNA AND AN INCOMING D4TTP AT PH 9.5 WITH CROSS-LINKING TO SECOND BASE TEMPLATE OVERHANG

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-1-1-mer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.112, V.113, D.187 Ligands: D4T.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.112, A:V.113, A:D.187 MG.2: 3 residues within 4Å: Chain A: D.445, E.480, D.500 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.445, A:E.480, A:D.500, H2O.2, H2O.3

1 x D4T: 2',3'-DEHYDRO-2',3'-DEOXY-THYMIDINE 5'-TRIPHOSPHATE(Non-covalent)

D4T.3: 16 residues within 4Å: Chain A: K.67, R.74, D.112, V.113, G.114, D.115, A.116, Y.117, Q.153, M.186, D.187, K.222 Chain C: A.5, C.6 Chain D: G.21 Ligands: MG.1 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:A.116 Hydrogen bonds: A:V.113, A:D.115, A:D.115, A:A.116, A:Q.153 Salt bridges: A:K.67, A:K.67, A:K.67, A:R.74, A:R.74, A:K.222, A:K.222, A:K.222 pi-Stacking: A:Y.117

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: Y.459, R.465, Q.466, K.467, D.490 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.466 GOL.5: 8 residues within 4Å: Chain A: T.405, E.406, Y.407, W.408 Chain B: K.347, Q.348, G.349, K.440 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:K.440, A:T.405, A:Y.407 GOL.6: 7 residues within 4Å: Chain B: W.282, E.344, Y.358, P.361, F.362, N.364, W.442 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.362, B:N.364, B:N.364 GOL.7: 8 residues within 4Å: Chain A: L.94, G.95, V.383 Chain B: Q.39, W.40, P.41, P.149, N.153 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.39, B:N.153, A:L.94 Water bridges: B:S.150 GOL.8: 3 residues within 4Å: Chain B: W.40, E.415, W.418 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Martinez, S.E. et al., Structure of HIV-1 reverse transcriptase/d4TTP complex: Novel DNA cross-linking site and pH-dependent conformational changes. Protein Sci. (2019)

Release Date

2018-08-15

Peptides

HIV-1 REVERSE TRANSCRIPTASE P66 SUBUNIT: A
HIV-1 REVERSE TRANSCRIPTASE P51 SUBUNIT: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

HIV-1 REVERSE TRANSCRIPTASE P66 SUBUNIT

HIV-1 REVERSE TRANSCRIPTASE P51 SUBUNIT

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