SMTL ID : 5yuw.1 (1 other biounit)

DNA polymerase IV - DNA ternary complex 6

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.12 Å

Oligo State

monomer

Ligands

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

TTP.1: 17 residues within 4Å: Chain A: D.9, M.10, D.11, C.12, F.13, F.14, S.43, T.44, R.50, S.56, D.104, K.158 Chain B: A.4 Chain C: C.18 Ligands: MG.2, MG.3, TTP.4 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.14, A:T.44 Hydrogen bonds: A:C.12, A:F.13, A:F.14 Water bridges: A:D.9, A:K.158 Salt bridges: A:R.50, A:R.50, A:K.158 TTP.4: 19 residues within 4Å: Chain A: D.9, M.10, D.11, C.12, F.13, F.14, S.43, T.44, R.50, S.56, D.104, E.105, K.158 Chain B: A.4, G.5 Chain C: C.18 Ligands: TTP.1, MG.2, MG.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.14, A:T.44 Hydrogen bonds: A:C.12, A:F.13, A:F.14 Water bridges: A:D.9, A:D.11, A:K.158 Salt bridges: A:R.50, A:R.50, A:K.158

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 7 residues within 4Å: Chain A: D.9, M.10, D.104, K.158 Ligands: TTP.1, MG.3, TTP.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.9, A:M.10, A:D.104 MG.3: 7 residues within 4Å: Chain A: D.9, D.104, E.105 Chain C: C.18 Ligands: TTP.1, MG.2, TTP.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.9, A:D.104, A:E.105

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kottur, J. et al., Pyrophosphate hydrolysis is an intrinsic and critical step of the DNA synthesis reaction. Nucleic Acids Res. (2018)

Release Date

2018-11-07

Peptides

DNA polymerase IV: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase IV

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