SMTL ID : 9emh.1

KOD-H4 DNA polymerase mutant in a binary complex with DNA:DNA containing two HNA nucleotides

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

monomer

Ligands

4 x IMD: IMIDAZOLE(Non-covalent)

IMD.1: 7 residues within 4Å: Chain A: R.266, E.330, L.333, V.344, S.347, T.349, L.352 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.266, A:S.347 IMD.4: 5 residues within 4Å: Chain A: F.545, E.580, Y.583, Y.594, R.606 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.594, A:Y.594 IMD.5: 5 residues within 4Å: Chain A: A.141, I.142, Y.209, D.215, D.315 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.142, A:Y.209 IMD.7: 3 residues within 4Å: Chain A: V.433, W.516, E.519 No protein-ligand interaction detected (PLIP)

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: K.118, E.251, W.342, D.343 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.251, A:D.343, H2O.1, H2O.2 MG.3: 6 residues within 4Å: Chain A: Y.110, E.111, A.368, P.369, N.370, R.503 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:A.368

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 4 residues within 4Å: Chain A: G.167, A.168, Y.180, M.313 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.168, A:A.168

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gutfreund, C. et al., Crystallographic Insights into a Mutant Archaeal B-Family Polymerase processing HNA. To Be Published

Release Date

2025-09-24

Peptides

DNA polymerase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase

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