4klq.1 | SWISS-MODEL Template Library

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SMTL ID : 4klq.1

Observing a DNA polymerase choose right from wrong.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 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: 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.9

5 PLIP interactions:

5 interactions with chain A

Hydrogen bonds: A:K.280, A:R.283, A:R.283
Salt bridges: A:R.283
pi-Stacking: A:H.34

1 x DTP: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE(Non-covalent)

DTP.2:

23 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: G.6, G.7
Chain C: C.10, A.11
Ligands: PPV.3, MN.4, MN.5, NA.7

8 PLIP interactions:

8 interactions with chain A

Hydrogen bonds: A:R.149, A:S.180, A:S.180, A:R.183, A:G.189, A:D.190
Water bridges: A:D.276
Salt bridges: A:R.183

1 x PPV: PYROPHOSPHATE(Non-covalent)

PPV.3:

11 residues within 4Å:

Chain A: R.149, G.179, S.180, R.183, G.189, D.190, D.192
Chain C: A.11
Ligands: DTP.2, MN.5, NA.7

9 PLIP interactions:

9 interactions with chain A

Hydrogen bonds: A:S.180, A:S.180, A:G.189, A:D.190
Water bridges: A:S.180, A:D.190, A:D.276
Salt bridges: A:R.149, A:R.183

3 x MN: MANGANESE (II) ION(Non-covalent)

MN.4:	6 residues within 4Å: Chain A: D.190, D.192, D.256 Chain C: A.11 Ligands: DTP.2, MN.5 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.190, A:D.192, A:D.256, H₂O.6, H₂O.7
MN.5:	5 residues within 4Å: Chain A: D.190, D.192 Ligands: DTP.2, PPV.3, MN.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.190, A:D.192, H₂O.1
MN.6:	1 residues within 4Å: Chain A: H.51 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.51

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

NA.7:	2 residues within 4Å: Ligands: DTP.2, PPV.3 No protein-ligand interaction detected (PLIP)
NA.8:	5 residues within 4Å: Chain A: T.101, V.103, G.105, I.106 Chain C: G.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.105, A:I.106, A:I.106
NA.9:	6 residues within 4Å: Chain A: K.60, K.61, L.62, P.63, V.65 Ligands: DG-DT-DC-DG-DG.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.65 Water bridges: A:K.61, A:L.62

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Freudenthal, B.D. et al., Observing a DNA polymerase choose right from wrong. Cell(Cambridge,Mass.) (2013)

Release Date

2013-07-17

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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