SMTL ID : 6wya.1

RTX (Reverse Transcription Xenopolymerase) in complex with a DNA duplex and dAMPNPP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.41 Å

Oligo State

monomer

Ligands

5 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.1: 4 residues within 4Å: Chain A: D.404, D.542 Chain C: T.20 Ligands: DZ4.5 No protein-ligand interaction detected (PLIP) MG.2: 2 residues within 4Å: Chain A: D.404 Ligands: DZ4.5 No protein-ligand interaction detected (PLIP) MG.3: 2 residues within 4Å: Chain A: D.141 Ligands: MG.4 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.141, H2O.1, H2O.3, H2O.7, H2O.9 MG.4: 5 residues within 4Å: Chain A: D.141, E.143, Y.311, D.315 Ligands: MG.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.141, A:E.143, A:D.315, H2O.9 MG.9: 2 residues within 4Å: Chain B: A.4, G.5 No protein-ligand interaction detected (PLIP)

1 x DZ4: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine(Non-covalent)

DZ4.5: 15 residues within 4Å: Chain A: F.405, S.407, L.408, Y.409, P.410, R.460, K.464, K.487, N.491, D.542 Chain B: T.3, A.4 Chain C: T.20 Ligands: MG.1, MG.2 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Y.409 Hydrogen bonds: A:S.407, A:Y.409, A:K.487, A:K.487, A:N.491 Water bridges: A:L.408, A:L.408, A:R.460, A:R.460, A:N.491, A:D.542 Salt bridges: A:R.460, A:K.464, A:K.487

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.6: 8 residues within 4Å: Chain A: D.4, T.5, D.6, E.251, K.253, S.340, W.342, D.343 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.4, A:K.253, A:K.253, A:S.340, A:D.343 Water bridges: A:T.5, A:I.118

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.7: 5 residues within 4Å: Chain A: R.585, D.598, E.599, G.601, K.632 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.585, A:R.585, A:D.598, A:K.632 EDO.10: 5 residues within 4Å: Chain A: V.589, R.743, R.746, A.747 Chain B: T.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.746, A:A.747

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.8: 6 residues within 4Å: Chain A: N.568, L.571, P.572, G.573, L.575, E.576 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:N.568, A:E.576 Hydrogen bonds: A:L.575

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Choi, W.S. et al., How a B family DNA polymerase has been evolved to copy RNA. Proc.Natl.Acad.Sci.USA (2020)

Release Date

2020-08-19

Peptides

DNA polymerase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase

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