SMTL ID : 8vbg.1

Kinetic intermediate states of HIV-1 RT DNA synthesis captured by cryo-EM

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

1 x F2A: 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]adenosine(Non-covalent)

F2A.1: 18 residues within 4Å: Chain A: K.67, K.72, R.74, L.76, D.112, V.113, G.114, D.115, A.116, Y.117, Q.153, D.187, K.222 Chain C: T.5, C.6, G.38 Ligands: MG.2, MG.3 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.117 Hydrogen bonds: A:R.74, A:R.74, A:D.115, A:D.115, A:A.116, A:Y.117, A:Q.153 Salt bridges: A:K.67, A:K.72, A:K.222 pi-Cation interactions: A:R.74

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.112, V.113, D.187 Ligands: F2A.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.112, A:V.113, A:D.187 MG.3: 3 residues within 4Å: Chain A: D.112 Chain C: G.38 Ligands: F2A.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.112, A:D.112

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vergara, S. et al., Structural basis of deoxynucleotide addition by HIV-1 RT during reverse transcription. Nat Commun (2024)

Release Date

2024-12-11

Peptides

HIV-1 reverse transcriptase/ribonuclease H P66 subunit: A
HIV-1 reverse transcriptase P51 subunit: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

HIV-1 reverse transcriptase/ribonuclease H P66 subunit

HIV-1 reverse transcriptase P51 subunit

Related Entries With Identical Sequence