3isd.1 | SWISS-MODEL Template Library

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SMTL ID : 3isd.1

Ternary complex of human DNA polymerase beta with an abasic site (THF): DAPCPP mismatch

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 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 C: C.1, C.2, G.3, A.4, C.5
Ligands: NA.3

1 PLIP interactions:

1 interactions with chain A

pi-Stacking: A:H.34

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

NA.2:	5 residues within 4Å: Chain A: T.101, V.103, S.104, I.106 Chain B: G.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.106, A:I.106
NA.3:	6 residues within 4Å: Chain A: K.60, K.61, L.62, P.63, V.65 Ligands: DG-DT-DC-DG-DG.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.61
NA.13:	1 residues within 4Å: Chain B: G.4 No protein-ligand interaction detected (PLIP)

8 x MN: MANGANESE (II) ION(Non-covalent)(Non-functional Binders)

MN.4:	4 residues within 4Å: Chain A: D.190, D.192 Ligands: MN.5, F2A.11 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.190, A:D.192, H₂O.4
MN.5:	6 residues within 4Å: Chain A: D.190, D.192, D.256 Chain B: C.10 Ligands: MN.4, F2A.11 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.190, A:D.192, A:D.256
MN.6:	2 residues within 4Å: Chain A: D.124 Ligands: EDO.12 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.124, H₂O.4
MN.7:	2 residues within 4Å: Chain A: H.285, E.288 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.285, A:E.288
MN.8:	1 residues within 4Å: Chain A: H.51 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.51
MN.9:	2 residues within 4Å: Chain A: E.249, H.252 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.252
MN.10:	1 residues within 4Å: Chain A: H.222 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.222, H₂O.6
MN.14:	1 residues within 4Å: Chain C: G.3 No protein-ligand interaction detected (PLIP)

1 x F2A: 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]adenosine(Non-covalent)

F2A.11:

18 residues within 4Å:

Chain A: G.179, S.180, R.183, S.188, G.189, D.190, D.192, Y.271, F.272, T.273, G.274, S.275, D.276, N.279, K.280
Chain B: C.10
Ligands: MN.4, MN.5

13 PLIP interactions:

13 interactions with chain A

Hydrogen bonds: A:S.180, A:S.180, A:R.183, A:R.183, A:G.189, A:D.190, A:Y.271, A:N.279, A:K.280, A:K.280
Water bridges: A:F.181, A:F.181, A:D.276

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.12:

4 residues within 4Å:

Chain A: E.123, D.124, K.127
Ligands: MN.6

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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