SMTL ID : 7omb.1

Crystal structure of KOD DNA Polymerase in a ternary complex with a p/t duplex containing an extended 5' single stranded template overhang

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

monomer

Ligands

1 x DTP: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE(Non-covalent)

DTP.1: 23 residues within 4Å: Chain A: D.404, F.405, R.406, S.407, L.408, Y.409, P.410, R.460, K.464, K.487, I.488, N.491, Y.494, G.495, T.541, D.542 Chain B: T.9, G.10 Chain C: C.12 Ligands: MG.3, MN.4, MN.6, EDO.11 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:Y.409 Hydrogen bonds: A:S.407, A:L.408, A:Y.409, A:N.491, A:N.491 Water bridges: A:D.404, A:R.460, A:R.460, A:R.460, A:K.487, A:K.487, A:E.578, A:E.578 Salt bridges: A:R.460, A:K.464, A:K.487, A:K.487, A:K.487

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.4, E.251, K.253, D.343 5 PLIP interactions: 5 Ligand-Water interactions Metal complexes: H2O.1, H2O.3, H2O.4, H2O.6, H2O.8 MG.3: 7 residues within 4Å: Chain A: Y.402, D.404, D.542, G.543 Chain C: C.12 Ligands: DTP.1, MN.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.404, A:D.542, H2O.6, H2O.7

4 x MN: MANGANESE (II) ION(Non-covalent)(Non-functional Binders)

MN.4: 7 residues within 4Å: Chain A: D.404, F.405, L.408, D.542 Ligands: DTP.1, MG.3, MN.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.404, A:F.405, A:D.542 MN.5: 3 residues within 4Å: Chain A: E.664 Chain B: T.17 Chain C: G.7 No protein-ligand interaction detected (PLIP) MN.6: 5 residues within 4Å: Chain A: D.404, F.405, E.580 Ligands: DTP.1, MN.4 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.404, A:E.580, H2O.2, H2O.2, H2O.2 MN.12: 1 residues within 4Å: Chain C: G.7 No protein-ligand interaction detected (PLIP)

5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.7: 10 residues within 4Å: Chain A: D.113, I.114, P.115, N.351, E.354, W.355, L.358, K.371, R.503 Chain B: G.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.351, A:E.354, A:K.371, A:R.503, A:R.503 EDO.8: 11 residues within 4Å: Chain A: P.36, Y.37, F.38, P.90, V.93, E.111, Y.112, D.113, I.114, F.116, R.119 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.37, A:Y.112, A:I.114 EDO.9: 5 residues within 4Å: Chain A: E.426, G.427, C.428, Y.431, R.440 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.426, A:G.427, A:C.428 EDO.10: 5 residues within 4Å: Chain A: G.395, L.396, F.587, A.747, F.748 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.396 EDO.11: 6 residues within 4Å: Chain B: T.9, G.10, T.11 Chain C: A.11, C.12 Ligands: DTP.1 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kropp, H.M. et al., Structural Basis for The Recognition of Deaminated Nucleobases by An Archaeal DNA Polymerase. Chembiochem (2021)

Release Date

2021-10-13

Peptides

DNA polymerase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase

Related Entries With Identical Sequence