SMTL ID : 4j2a.1

RB69 DNA Polymerase L415A Ternary Complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

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

TTP.1: 17 residues within 4Å: Chain A: D.411, L.412, T.413, S.414, A.415, Y.416, P.417, R.482, K.560, N.564, Y.567, D.623 Chain B: A.4, G.5 Chain C: C.13 Ligands: CA.2, CA.3 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:Y.416 Hydrogen bonds: A:D.411, A:D.411, A:L.412, A:S.414, A:A.415, A:Y.416, A:N.564 Water bridges: A:R.482, A:K.486, A:K.486, A:K.560, A:K.560 Salt bridges: A:R.482, A:K.486, A:K.560, A:K.560, A:K.560

7 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.2: 5 residues within 4Å: Chain A: D.411, L.412, D.623 Ligands: TTP.1, CA.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.411, A:L.412, A:D.623 CA.3: 5 residues within 4Å: Chain A: D.411, D.623 Chain C: C.13 Ligands: TTP.1, CA.2 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.623, H2O.32 CA.4: 3 residues within 4Å: Chain A: N.505, N.507, K.531 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:N.505, A:K.531, H2O.9, H2O.12, H2O.26 CA.5: 1 residues within 4Å: Chain A: E.716 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.716, H2O.2, H2O.4, H2O.12, H2O.16 CA.6: 1 residues within 4Å: Chain A: E.116 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.116, A:E.116, H2O.11, H2O.18 CA.7: 3 residues within 4Å: Chain A: L.857, D.860, D.861 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.860, A:D.861 CA.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xia, S. et al., Alteration in the cavity size adjacent to the active site of RB69 DNA polymerase changes its conformational dynamics. Nucleic Acids Res. (2013)

Release Date

2014-02-19

Peptides

DNA polymerase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase