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SMTL ID : 5wnx.1

DNA polymerase beta substrate complex with incoming 6-TdGTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

monomer

Ligands

1 x DG- DT- DC- DG- DG: DNA (5'-D(P*GP*TP*CP*GP*G)-3')(Non-covalent)

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

17 residues within 4Å:

Chain A: C.1, C.2, G.3, A.4, C.5
Chain C: H.34, K.35, A.38, L.62, P.63, G.64, V.65, G.66, T.67, K.68, I.69
Ligands: NA.3

3 PLIP interactions:

3 interactions with chain C

Hydrogen bonds: C:H.34, C:R.283
pi-Stacking: C:H.34

2 x NA: SODIUM ION(Non-functional Binders)

NA.2:	4 residues within 4Å: Chain B: G.9 Chain C: T.101, V.103, I.106 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:V.103
NA.3:	4 residues within 4Å: Chain C: K.60, L.62, V.65 Ligands: DG-DT-DC-DG-DG.1 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:V.65, C:V.65

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.4:

3 residues within 4Å:

Chain C: N.294, T.297, R.299

Ligand excluded by PLIP

1 x SGT: 2-amino-9-{2-deoxy-5-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-erythro-pentofuranosyl}-1,9-dihydro-6H-purine-6-thione(Non-covalent)

SGT.5:

19 residues within 4Å:

Chain A: C.6, G.7
Chain B: C.10
Chain C: G.179, S.180, R.183, S.188, G.189, D.190, D.192, Y.271, F.272, T.273, G.274, D.276, N.279, R.283
Ligands: CA.6, CA.7

12 PLIP interactions:

12 interactions with chain C

Hydrogen bonds: C:R.149, C:R.149, C:S.180, C:S.180, C:S.180, C:R.183, C:G.189, C:D.190, C:N.279, C:R.283
Water bridges: C:D.276
Salt bridges: C:R.183

2 x CA: CALCIUM ION(Non-covalent)

CA.6:	6 residues within 4Å: Chain B: C.10 Chain C: D.190, D.192, D.256 Ligands: SGT.5, CA.7 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.190, C:D.190, C:D.192, C:D.256, H₂O.1
CA.7:	4 residues within 4Å: Chain C: D.190, D.192 Ligands: SGT.5, CA.6 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.190, C:D.190, C:D.192, H₂O.1

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Schaich, M.A. et al., Structures of a DNA Polymerase Inserting Therapeutic Nucleotide Analogues. Chem. Res. Toxicol. (2017)

Release Date

2017-09-13

Peptides

DNA polymerase beta: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

DNA polymerase beta

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