3isb.1 | SWISS-MODEL Template Library

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SMTL ID : 3isb.1

Binary complex of human DNA polymerase beta with a gapped DNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

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

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

17 residues within 4Å:

Chain A: K.35, A.38, Y.39, L.62, P.63, G.64, V.65, G.66, T.67, K.68, I.69
Chain B: C.1, C.2, G.3, A.4, C.5
Ligands: NA.3

2 PLIP interactions:

2 interactions with chain A

Water bridges: A:H.34
pi-Stacking: A:H.34

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

NA.2:	7 residues within 4Å: Chain A: T.101, V.103, S.104, G.105, I.106 Chain C: G.9 Ligands: NA.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.105, A:I.106, A:I.106
NA.3:	4 residues within 4Å: Chain A: K.60, L.62, V.65 Ligands: DG-DT-DC-DG-DG.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.60, A:V.65
NA.4:	2 residues within 4Å: Chain A: T.101 Ligands: NA.2 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.27, A:K.27
NA.5:	1 residues within 4Å: Chain A: S.171 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.171 Water bridges: A:D.170

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.6:

5 residues within 4Å:

Chain B: C.8, G.9
Chain C: T.6, G.7, C.8

No protein-ligand interaction detected (PLIP)

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Beard, W.A. et al., DNA polymerase beta substrate specificity: side chain modulation of the "A-rule". J.Biol.Chem. (2009)

Release Date

2009-09-15

Peptides

DNA polymerase beta: 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 beta

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