6crb.1 | SWISS-MODEL Template Library

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SMTL ID : 6crb.1

Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CF2, beta, gamma dATP analogue

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

monomer

Ligands

1 x DG- DT- DC- DG- DG: Downstream Primer Strand(Non-covalent)

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

18 residues within 4Å:

Chain A: H.34, 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.5

6 PLIP interactions:

6 interactions with chain A

Hydrophobic interactions: A:K.280, A:K.280
Hydrogen bonds: A:R.283
Water bridges: A:H.34, A:N.37
pi-Stacking: A:H.34

1 x VA6: 9-{2-deoxy-5-O-[(S)-{[(S)-[difluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-alpha-D-erythro-pentofuranosyl}-9H-purin-6-amine(Non-covalent)

VA6.2:

20 residues within 4Å:

Chain A: R.149, 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
Chain B: T.6, G.7
Chain C: C.10
Ligands: MG.3, NA.6

9 PLIP interactions:

9 interactions with chain A

Hydrogen bonds: A:R.149, A:S.180, A:S.180, A:R.183, A:R.183, A:G.189, A:D.190, A:G.274
Halogen bonds: A:R.183

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3:

3 residues within 4Å:

Chain A: D.190, D.192
Ligands: VA6.2

3 PLIP interactions:

2 interactions with chain A, 1 Ligand-Water interactions

Metal complexes: A:D.190, A:D.192, H₂O.2

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

NA.4:	5 residues within 4Å: Chain A: T.101, V.103, S.104, I.106 Chain C: G.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.103, A:G.105, A:I.106
NA.5:	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.6:	5 residues within 4Å: Chain A: D.190, D.192, D.256 Chain C: C.10 Ligands: VA6.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.192

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Batra, V.K. et al., Mapping Functional Substrate-Enzyme Interactions in the pol beta Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs. Biochemistry (2018)

Release Date

2018-07-18

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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