SMTL ID : 6p7e.4 (3 other biounits)

Structure of T7 DNA Polymerase Bound to a Primer/Template DNA and a Peptide that Mimics the C-terminal Tail of the Primase-Helicase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

hetero-1-1-mer

Ligands

2 x TTP: THYMIDINE-5'-TRIPHOSPHATE(Non-covalent)

TTP.1: 9 residues within 4Å: Chain A: A.7, A.8, N.9, A.10, L.11, Y.64, W.160, D.174 Ligands: MG.4 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.11, A:W.160 Hydrogen bonds: A:A.8, A:A.8 pi-Stacking: A:W.160, A:W.160 TTP.5: 17 residues within 4Å: Chain A: R.429, D.475, A.476, G.478, L.479, E.480, H.506, R.518, K.522, Y.526, Y.530, D.654 Chain C: A.21 Chain D: A.4, T.5 Ligands: MG.2, MG.3 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:E.480, A:Y.526 Hydrogen bonds: A:R.429, A:D.475, A:G.478, A:L.479, A:E.480, A:Y.526, A:D.654 Salt bridges: A:H.506, A:H.506, A:R.518, A:K.522, A:K.522, A:K.522 pi-Stacking: A:Y.526

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.475, A.476, D.654 Ligands: MG.3, TTP.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.475, A:A.476, A:D.654 MG.3: 4 residues within 4Å: Chain A: D.475, D.654 Ligands: MG.2, TTP.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.475, A:D.475, A:D.654, A:D.654 MG.4: 3 residues within 4Å: Chain A: H.59, D.65 Ligands: TTP.1 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Foster, B.M. et al., Combined Solution and Crystal Methods Reveal the Electrostatic Tethers That Provide a Flexible Platform for Replication Activities in the Bacteriophage T7 Replisome. Biochemistry (2019)

Release Date

2020-03-04

Peptides

DNA-directed DNA polymerase: A
TrxA: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
H

DNA-directed DNA polymerase

TrxA

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