SMTL ID : 5omf.1

Closed, ternary structure of KOD DNA polymerase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

monomer

Ligands

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 5 residues within 4Å: Chain A: D.404, F.405, E.580 Ligands: MN.2, DTP.10 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.404, A:E.580, H2O.1, H2O.2, H2O.4 MN.2: 7 residues within 4Å: Chain A: D.404, F.405, L.408, D.542 Ligands: MN.1, MG.7, DTP.10 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.404, A:F.405, A:D.542

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

EDO.3: 9 residues within 4Å: Chain A: D.614, W.615, I.662, E.664, Y.701, Q.736 Chain B: G.11, T.12 Chain C: G.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.614, A:Q.736 EDO.4: 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.5: 9 residues within 4Å: Chain A: D.4, T.5, K.118, Q.242, E.251, K.253, S.340, W.342, D.343 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.4, A:E.251 Water bridges: A:K.253 EDO.6: 9 residues within 4Å: Chain A: F.75, L.76, P.369, R.380, P.420, R.503, W.504, Y.505, C.506 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.504

1 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 6 residues within 4Å: Chain A: Y.402, D.404, D.542 Chain C: C.12 Ligands: MN.2, DTP.10 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.404, A:D.542, H2O.6, H2O.8

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 8 residues within 4Å: Chain A: Y.402, F.545, E.580, Y.583, Y.594, T.604, R.606 Chain C: C.12 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.402, A:Y.594, A:R.606, A:R.606 GOL.9: 5 residues within 4Å: Chain A: E.426, G.427, C.428, Y.431, R.440 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.426, A:G.427, A:R.440, A:R.440 GOL.11: 6 residues within 4Å: Chain B: G.8, C.9 Chain C: C.6, G.7, G.8, C.9 No protein-ligand interaction detected (PLIP)

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

DTP.10: 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, S.492, Y.494, G.495, T.541, D.542 Chain B: T.4, G.5 Chain C: C.12 Ligands: MN.1, MN.2, MG.7 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:Y.409 Hydrogen bonds: A:F.405, A:S.407, A:L.408, A:Y.409, A:N.491, A:N.491 Water bridges: A:S.407, A:S.407, A:R.460, A:R.460, A:R.460, A:K.464, A:K.464 Salt bridges: A:R.460, A:K.464, A:K.487, A:K.487, A:K.487

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kropp, H.M. et al., Crystal structures of ternary complexes of archaeal B-family DNA polymerases. PLoS ONE (2017)

Release Date

2017-12-20

Peptides

DNA polymerase,DNA polymerase,DNA polymerase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase,DNA polymerase,DNA polymerase

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