2p66.1 | SWISS-MODEL Template Library

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SMTL ID : 2p66.1

Human DNA Polymerase beta complexed with tetrahydrofuran (abasic site) containing DNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

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

3DR-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, Y.39, L.62, G.64, V.65, G.66, T.67, K.68, I.69
Ligands: NA.4

1 PLIP interactions:

1 interactions with chain C

Hydrophobic interactions: C:K.68
Hydrogen bonds: C:K.35
Salt bridges: C:K.68
pi-Stacking: C:H.34

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

NA.2:	3 residues within 4Å: Chain B: C.11 Chain C: D.190, D.192 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.190
NA.3:	5 residues within 4Å: Chain B: G.9 Chain C: T.101, V.103, S.104, I.106 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:I.106, C:I.106
NA.4:	4 residues within 4Å: Chain C: K.60, L.62, V.65 Ligands: 3DR-DG-DT-DC-DG-DG.1 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:V.65, C:V.65

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5:

5 residues within 4Å:

Chain C: R.149, S.180, S.188, G.189, D.190

5 PLIP interactions:

5 interactions with chain C

Hydrogen bonds: C:S.180, C:S.180, C:G.189, C:D.190
Salt bridges: C:R.149

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Prasad, R. et al., Structural insight into the DNA Polymerase beta deoxyribose phosphate lyase mechanism. DNA REPAIR (2005)

Release Date

2007-04-10

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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