SMTL ID : 7oz5.1 (1 other biounit)

Crystal structure of HIV-1 reverse transcriptase with a double stranded DNA in complex with fragment 166 at the transient P-pocket.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.37 Å

Oligo State

hetero-1-1-mer

Ligands

1 x GLC- FRU: beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose(Non-covalent)

GLC-FRU.1: 10 residues within 4Å: Chain B: V.37, W.40, D.92, R.94, E.95, K.98, K.411, E.415, E.429, W.430 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:D.92, B:D.92, B:K.411, B:W.430, B:E.95, B:E.95, B:E.95, B:K.98, B:E.429, B:W.430, B:W.430

9 x CD: CADMIUM ION(Non-covalent)(Non-functional Binders)

CD.2: 3 residues within 4Å: Chain A: D.445, E.480, D.500 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.445, A:D.445, A:E.480, A:D.500, A:D.500 CD.3: 3 residues within 4Å: Chain A: Q.176, H.210, R.213 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.210 CD.4: 3 residues within 4Å: Chain A: H.541, D.551, S.555 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.541, A:D.551, A:D.551 CD.5: 1 residues within 4Å: Chain B: E.313 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.313, B:E.313 CD.6: 1 residues within 4Å: Chain B: H.224 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.224 CD.7: 3 residues within 4Å: Chain B: E.240, E.249, H.251 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.240, B:E.240, B:E.249, B:E.249, B:H.251 CD.8: 2 residues within 4Å: Chain C: G.9, C.10 No protein-ligand interaction detected (PLIP) CD.9: 2 residues within 4Å: Chain C: G.20, G.21 No protein-ligand interaction detected (PLIP) CD.10: 2 residues within 4Å: Chain D: C.13, G.14 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, A.K. et al., Sliding of HIV-1 reverse transcriptase over DNA creates a transient P pocket - targeting P-pocket by fragment screening. Nat Commun (2021)

Release Date

2021-12-08

Peptides

Reverse transcriptase/ribonuclease H: A
Gag-Pol polyprotein: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Reverse transcriptase/ribonuclease H

Gag-Pol polyprotein

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