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SMTL ID : 6dia.1

DNA polymerase beta substrate complex with templating cytosine and incoming Fapy-dGTP analog

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

monomer

Ligands

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

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

17 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

2 PLIP interactions:

2 interactions with chain A

Water bridges: A:N.37
pi-Stacking: A:H.34

1 x GKS: 1-[2-amino-5-(formylamino)-6-oxo-1,6-dihydropyrimidin-4-yl]-2,5-anhydro-1,3-dideoxy-6-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-D-ribo-hexitol(Non-covalent)

GKS.2:

21 residues within 4Å:

Chain A: R.149, G.179, S.180, R.183, S.188, G.189, D.190, D.192, K.234, R.258, Y.271, F.272, G.274, S.275, D.276, N.279
Chain B: C.6, G.7
Chain C: C.10
Ligands: CA.4, NA.7

22 PLIP interactions:

22 interactions with chain A

Hydrophobic interactions: A:Y.271
Hydrogen bonds: A:S.180, A:S.180, A:S.180, A:G.189, A:D.190, A:K.234, A:R.258, A:R.258
Water bridges: A:G.179, A:D.190, A:D.256, A:D.256, A:Y.271, A:Y.271, A:D.276, A:D.276, A:N.279
Salt bridges: A:R.149, A:R.183, A:D.192
pi-Stacking: A:F.272

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

NA.3:	4 residues within 4Å: Chain A: T.101, V.103, 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.7:	3 residues within 4Å: Chain A: D.190 Chain C: C.10 Ligands: GKS.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.190 Water bridges: A:D.190

3 x CA: CALCIUM ION(Non-covalent)

CA.4:	3 residues within 4Å: Chain A: D.190, D.192 Ligands: GKS.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.190, A:D.192, A:D.192, H₂O.1, H₂O.6
CA.5:	1 residues within 4Å: Chain A: D.145 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.145, H₂O.3, H₂O.6, H₂O.7, H₂O.9
CA.6:	2 residues within 4Å: Chain A: E.295 Chain B: C.6 No protein-ligand interaction detected (PLIP)

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Smith, M.R. et al., A guardian residue hinders insertion of a Fapy•dGTP analog by modulating the open-closed DNA polymerase transition. Nucleic Acids Res. (2019)

Release Date

2019-01-30

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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