SMTL ID : 7om3.1

Crystal structure of KOD DNA Polymerase in a binary complex with Hypoxanthine containing template

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

monomer

Ligands

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.1: 11 residues within 4Å: Chain A: V.127, R.335, L.336, G.338, F.356, R.359, K.360, D.455, L.456, E.459, R.482 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.335, A:K.360, A:E.459, A:R.482 Water bridges: A:R.482

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

EDO.2: 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: C.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.113, A:E.354, A:K.371, A:R.503, A:R.503 EDO.3: 5 residues within 4Å: Chain A: G.167, A.168, Y.180, M.313, K.317 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.168, A:K.317 EDO.4: 2 residues within 4Å: Chain A: D.182, V.183 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.183, A:V.183

2 x BR: BROMIDE ION(Non-covalent)

BR.5: 5 residues within 4Å: Chain A: I.618, K.649, V.655, P.656, K.659 Ligand excluded by PLIP BR.6: 3 residues within 4Å: Chain A: R.460, K.464, K.487 Ligand excluded by PLIP

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 8 residues within 4Å: Chain A: A.141, I.142, Y.209, N.210, F.214, D.215, L.275, D.315 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:I.142, A:D.215, A:D.215, A:D.315 Water bridges: A:Y.209, A:Y.209

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,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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