5ewe.1 | SWISS-MODEL Template Library

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SMTL ID : 5ewe.1

Ternary complex of human DNA polymerase eta inserting rCTP opposite template G

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.66 Å

Oligo State

monomer

Ligands

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

DA-DG-DC-DG-DT-DC-DA-DT.1:

26 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, R.380, L.384, R.385, R.386
Chain B: A.5, T.6, G.7, A.8, C.9, G.10, C.11, T.12
Ligands: CTP.2, CA.4

Protein-ligand interaction information (PLIP) not available

1 x CTP: CYTIDINE-5'-TRIPHOSPHATE(Non-covalent)

CTP.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: G.4, A.5
Ligands: DA-DG-DC-DG-DT-DC-DA-DT.1, CA.3, CA.4

14 PLIP interactions:

14 interactions with chain A

Hydrogen bonds: A:C.19, A:F.20, A:Y.55, A:R.64
Water bridges: A:R.58, A:R.58, A:R.58, A:R.58, A:R.64, A:R.64
Salt bridges: A:R.58, A:R.58, A:R.64, A:K.234

2 x CA: CALCIUM ION(Non-covalent)

CA.3:	5 residues within 4Å: Chain A: D.16, M.17, D.118 Ligands: CTP.2, CA.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.16, A:M.17, A:D.118
CA.4:	6 residues within 4Å: Chain A: D.16, D.118, E.119 Ligands: DA-DG-DC-DG-DT-DC-DA-DT.1, CTP.2, CA.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.118, A:E.119

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5:	5 residues within 4Å: Chain A: P.247, F.250, S.251, G.279, E.280 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.250 Water bridges: A:E.280, A:T.282, A:T.282
GOL.6:	0 residues within 4Å: (No contacts) 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.290, A:E.295

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Su, Y. et al., Mechanism of Ribonucleotide Incorporation by Human DNA Polymerase eta. J.Biol.Chem. (2016)

Release Date

2016-01-13

Peptides

DNA polymerase eta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

DNA polymerase eta

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