SMTL ID : 5vu8.1

TNA polymerase, closed ternary complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

monomer

Ligands

1 x 9O7: [(3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-oxolan-3-yl] [oxidanyl(phosphonooxy)phosphoryl] hydrogen phosphate(Non-covalent)

9O7.1: 19 residues within 4Å: Chain A: D.404, F.405, R.406, S.407, Y.409, R.460, K.487, I.488, N.491, T.541, D.542, E.578, E.580 Chain B: T.4, T.5 Chain C: X.12 Ligands: MG.2, MG.3, MG.4 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:D.404, A:S.407, A:N.491, A:N.491, A:T.541, A:D.542 Salt bridges: A:R.460, A:R.460, A:K.487, A:K.487

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: Y.402, D.542 Chain C: X.12 Ligands: 9O7.1 No protein-ligand interaction detected (PLIP) MG.3: 3 residues within 4Å: Chain A: E.578, E.580 Ligands: 9O7.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.580, A:E.580 MG.4: 4 residues within 4Å: Chain A: K.487, R.606 Chain C: X.12 Ligands: 9O7.1 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:?.12

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chim, N. et al., Structural basis for TNA synthesis by an engineered TNA polymerase. Nat Commun (2017)

Release Date

2017-12-06

Peptides

DNA polymerase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase

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