SMTL ID : 8gkr.1

Crystal structure of human DNA polymerase eta incorporating 5F-dUTP across dA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.78 Å

Oligo State

monomer

Ligands

1 x DA- DG- DT- DG- DT- DG- DA- DG: DNA (5'-D(*AP*GP*TP*GP*TP*GP*AP*G)-3')(Non-covalent)

DA-DG-DT-DG-DT-DG-DA-DG.1: 28 residues within 4Å: Chain A: S.113, D.115, E.116, K.224, I.255, R.256, S.257, L.258, G.259, G.260, K.261, L.262, R.377, L.381, R.382, R.383, C.384 Chain B: A.4, C.5, T.6, C.7, A.8, C.9, A.10, C.11, T.12 Ligands: B7P.2, CA.8 Protein-ligand interaction information (PLIP) not available

1 x B7P: 2'-deoxy-5-fluorouridine 5'-(tetrahydrogen triphosphate)(Non-covalent)

B7P.2: 19 residues within 4Å: Chain A: D.13, M.14, D.15, C.16, F.17, F.18, I.48, A.49, Y.52, R.55, R.61, I.114, D.115, K.231 Chain B: T.3, A.4 Ligands: DA-DG-DT-DG-DT-DG-DA-DG.1, CA.8, CA.9 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.18 Hydrogen bonds: A:C.16, A:F.17, A:F.18, A:Y.52, A:Y.52 Salt bridges: A:R.55, A:R.55, A:R.61, A:R.61, A:R.61, A:K.231

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: S.257, N.294, W.297 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.257, A:S.257, A:N.294 GOL.4: 5 residues within 4Å: Chain A: P.244, F.247, S.248, G.276, E.277 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.247 GOL.5: 3 residues within 4Å: Chain A: E.148, L.229, N.230 No protein-ligand interaction detected (PLIP) GOL.6: 1 residues within 4Å: Chain A: R.303 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.303 GOL.7: 1 residues within 4Å: Chain A: E.283 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.283, A:Q.287

2 x CA: CALCIUM ION(Non-covalent)

CA.8: 6 residues within 4Å: Chain A: D.13, D.115, E.116 Ligands: DA-DG-DT-DG-DT-DG-DA-DG.1, B7P.2, CA.9 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.13, A:E.116 CA.9: 6 residues within 4Å: Chain A: D.13, M.14, D.15, D.115 Ligands: B7P.2, CA.8 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.13, A:D.13, A:M.14, A:D.115

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jung, H., Crystal structure of human DNA polymerase eta incorporating 5F-dUTP across dA. To Be Published

Release Date

2023-09-20

Peptides

DNA polymerase eta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase eta

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