SMTL ID : 3kd5.1

Closed ternary complex of an RB69 gp43 fingers domain mutant complexed with an acyclic GMP terminated primer template pair and phosphonoformic acid.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.69 Å

Oligo State

monomer

Ligands

1 x PPF: PHOSPHONOFORMIC ACID(Non-covalent)

PPF.1: 10 residues within 4Å: Chain B: X.14 Chain C: D.411, L.412, T.413, S.414, L.415, R.482, K.560, D.623 Ligands: MG.3 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:S.414, C:L.415, C:R.482, C:R.482, C:K.560 Water bridges: C:D.411, C:S.414, C:K.486, C:K.486, C:N.564, C:N.564, C:N.564

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain B: A.13, X.14 Chain C: D.411, D.623 Ligands: MG.3 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.411, C:D.411, C:D.623, H2O.2, H2O.8 MG.3: 6 residues within 4Å: Chain B: X.14 Chain C: D.411, L.412, D.623 Ligands: PPF.1, MG.2 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.411, C:L.412, C:D.623 MG.4: 4 residues within 4Å: Chain C: D.114, E.116, N.324, D.327 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.114, C:E.116, H2O.8

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zahn, K.E. et al., Phosphonoformic acid inhibits viral replication by trapping the closed form of the DNA polymerase. J.Biol.Chem. (2011)

Release Date

2011-04-13

Peptides

DNA polymerase: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
E

DNA polymerase

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