SMTL ID : 9qrl.1

DNA polymerase with inhibitor #2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.20 Å

Oligo State

monomer

Ligands

1 x DT- DA- DA: DNA (5'-D(P*TP*AP*A)-3')(Non-covalent)

DT-DA-DA.1: 18 residues within 4Å: Chain A: A.455, T.456, G.458, L.459, L.500, T.501, N.534, F.537, L.562, R.566, R.574, F.575, G.576, L.577, D.597, R.638, Q.702 Ligands: MG.6 Protein-ligand interaction information (PLIP) not available

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 6 residues within 4Å: Chain A: H.366, H.368, E.425, N.764, H.766 Ligands: ZN.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.366, A:H.368 ZN.3: 4 residues within 4Å: Chain A: H.368, D.375, H.400, H.766 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.375, A:H.400, A:H.766 ZN.4: 5 residues within 4Å: Chain A: H.400, E.425, H.641, C.691 Ligands: ZN.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.425, A:H.641, A:C.691, H2O.1 ZN.5: 4 residues within 4Å: Chain A: C.940, C.943, C.965, C.968 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.940, A:C.943, A:C.965, A:C.968

2 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 4 residues within 4Å: Chain A: D.538, D.597 Ligands: DT-DA-DA.1, DT-DA-DA.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.597 MG.7: 4 residues within 4Å: Chain A: D.994, D.996, K.1117, D.1119 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.994, A:D.996, A:D.1119

1 x 01: 2-[(3,4-dichlorophenyl)methylamino]-7-(2-morpholin-4-ylethyl)-1~{H}-purin-6-one

01.8: 11 residues within 4Å: Chain A: E.1178, S.1203, H.1207, Y.1296, F.1298, H.1302, A.1303, Y.1306 Chain B: T.33 Chain C: C.9, A.10 4 PLIP interactions: 4 interactions with chain A pi-Stacking: A:H.1207, A:H.1302, A:Y.1306 pi-Cation interactions: A:Y.1296

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lamers, M.H. et al., DNA polymerase with inhibitor. To Be Published

Release Date

2025-09-24

Peptides

DNA polymerase III PolC-type: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase III PolC-type

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