SMTL ID : 6w5x.1

Crystal structure of human polymerase eta complexed with N7-benzylguanine and dCTP*

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.59 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: X.4, C.5, T.6, C.7, A.8, C.9, A.10, C.11, T.12 Ligands: 0KX.3, MN.4 Protein-ligand interaction information (PLIP) not available

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 1 residues within 4Å: Chain A: E.283 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.283

1 x 0KX: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine(Non-covalent)

0KX.3: 18 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: X.4 Ligands: DA-DG-DT-DG-DT-DG-DA-DG.1, MN.4, MN.5 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.18 Hydrogen bonds: A:C.16, A:F.17, A:F.18, A:Y.52, A:R.61, A:R.61 Salt bridges: A:R.55, A:K.231

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

MN.4: 7 residues within 4Å: Chain A: D.13, S.113, D.115, E.116 Ligands: DA-DG-DT-DG-DT-DG-DA-DG.1, 0KX.3, MN.5 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.13, A:D.115, A:D.115, A:E.116, H2O.1 MN.5: 6 residues within 4Å: Chain A: D.13, M.14, D.115, K.231 Ligands: 0KX.3, MN.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.13, A:M.14, A:D.115

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jung, H. et al., Crystal structure of human polymerase eta complexed with N7-benzylguanine and dCTP*. To Be Published

Release Date

2021-03-17

Peptides

DNA polymerase eta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase eta

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