SMTL ID : 3mr3.1

Human DNA polymerase eta - DNA ternary complex with the 3'T of a CPD in the active site (TT1)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

1 x DC- DA- DG- DC- DG- DT- DC- DA- DT: DNA (5'-D(*CP*AP*GP*CP*GP*TP*CP*AP*T)-3')(Non-covalent)

DC-DA-DG-DC-DG-DT-DC-DA-DT.1: 34 residues within 4Å: Chain A: S.116, D.118, E.119, K.227, I.258, R.259, S.260, L.261, G.262, G.263, K.264, L.265, T.367, Q.368, R.380, L.381, L.384, R.385, R.386, C.387, C.388, A.389, K.431 Chain B: T.3, A.4, T.5, G.6, A.7, C.8, G.9, C.10, T.11 Ligands: DZ4.2, MG.4 Protein-ligand interaction information (PLIP) not available

2 x DZ4: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine(Non-covalent)

DZ4.2: 19 residues within 4Å: Chain A: D.16, M.17, D.18, C.19, F.20, F.21, I.51, A.52, Y.55, R.58, R.64, I.117, D.118, K.234 Chain B: T.3, A.4 Ligands: DC-DA-DG-DC-DG-DT-DC-DA-DT.1, MG.3, MG.4 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:F.21 Hydrogen bonds: A:M.17, A:C.19, A:F.20, A:F.21, A:Y.55, A:R.64, A:R.64 Water bridges: A:D.16, A:D.16, A:Y.55, A:R.58, A:R.58, A:R.58, A:R.58, A:R.58, A:S.116 Salt bridges: A:R.58, A:K.234 DZ4.11: 5 residues within 4Å: Chain A: S.260, L.265, K.296, N.297, W.300 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.260, A:N.297 pi-Stacking: A:W.300, A:W.300, A:W.300

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain A: D.16, M.17, D.118, K.234 Ligands: DZ4.2, MG.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.16, A:M.17, A:D.118 MG.4: 7 residues within 4Å: Chain A: D.16, S.116, D.118, E.119 Ligands: DC-DA-DG-DC-DG-DT-DC-DA-DT.1, DZ4.2, MG.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.16, A:D.118, A:E.119, H2O.1

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: P.247, F.250, S.251, G.279, E.280 Ligands: GOL.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.247 GOL.6: 3 residues within 4Å: Chain A: N.29, P.30, H.31 No protein-ligand interaction detected (PLIP) GOL.7: 3 residues within 4Å: Chain A: P.30, H.31, K.35 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.31, A:K.35 Water bridges: A:H.31, A:K.35 GOL.8: 2 residues within 4Å: Chain A: L.345, H.396 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.396 Water bridges: A:Q.346 GOL.9: 1 residues within 4Å: Chain A: E.104 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.104, A:E.104 Water bridges: A:E.101 GOL.10: 7 residues within 4Å: Chain A: H.243, V.246, P.247, T.282, C.305, R.306 Ligands: GOL.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.243

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Biertumpfel, C. et al., Structure and mechanism of human DNA polymerase eta. Nature (2010)

Release Date

2010-06-30

Peptides

DNA polymerase eta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase eta

Related Entries With Identical Sequence