4o9m.1 | SWISS-MODEL Template Library

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SMTL ID : 4o9m.1

Human DNA polymerase beta complexed with adenylated tetrahydrofuran (abasic site) containing DNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 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:

18 residues within 4Å:

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

3 PLIP interactions:

3 interactions with chain C

Water bridges: C:H.34, C:K.280
pi-Stacking: C:H.34

1 x 2RW: [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3S)-3-hydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate(Non-covalent)

2RW.2:

7 residues within 4Å:

Chain C: K.35, K.68, E.71, K.72, K.84
Ligands: DG-DT-DC-DG-DG.1, DG-DT-DC-DG-DG.1

9 PLIP interactions:

9 interactions with chain C

Hydrophobic interactions: C:K.68
Hydrogen bonds: C:K.35, C:K.72, C:K.84
Water bridges: C:E.26, C:K.68, C:E.71
Salt bridges: C:K.68, C:K.68

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

NA.3:	6 residues within 4Å: Chain B: G.9 Chain C: T.101, V.103, S.104, G.105, I.106 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:V.103, C:G.105, C:I.106
NA.4:	4 residues within 4Å: Chain C: K.60, L.62, V.65 Ligands: DG-DT-DC-DG-DG.1 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.64, C:V.65, C:V.65

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Caglayan, M. et al., Role of polymerase beta in complementing aprataxin deficiency during abasic-site base excision repair. Nat.Struct.Mol.Biol. (2014)

Release Date

2014-04-30

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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