SMTL ID : 4kpy.2 (1 other biounit)

DNA binding protein and DNA complex structure

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.41 Å

Oligo State

monomer

Ligands

1 x DA- DC- DA- DA- DC- DC: DNA (5'-D(*TP*AP*TP*AP*CP*AP*AP*CP*C)-3')(Non-covalent)

DA-DC-DA-DA-DC-DC.1: 23 residues within 4Å: Chain A: Y.43, P.44, A.47, R.51, R.81, R.114, D.546, G.547, R.548, V.573, R.574, K.575, S.576, G.577, K.618 Chain B: G.11, G.12, T.13, T.14, G.15, T.16 Chain C: T.1 Ligands: MN.3 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:G.481, A:D.546, A:D.660 Water bridges: A:A.479, A:R.482, A:D.660, A:D.660, A:D.660, A:D.660, A:K.664, A:K.664 Salt bridges: A:K.575, A:K.664, A:K.664, A:R.668

1 x DT: THYMIDINE-5'-MONOPHOSPHATE(Non-covalent)

DT.2: 11 residues within 4Å: Chain A: Y.197, R.200, W.202, L.223, Y.226, H.227, K.230, R.232, I.254, P.255, H.256 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.226 Hydrogen bonds: A:N.195, A:Y.226, A:H.256 Salt bridges: A:R.200, A:H.227, A:R.232 pi-Stacking: A:Y.226

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

MN.3: 6 residues within 4Å: Chain A: D.478, A.479, D.546 Chain C: T.1 Ligands: DA-DC-DA-DA-DC-DC.1, MN.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.478, A:D.546, H2O.1, H2O.6 MN.4: 4 residues within 4Å: Chain A: D.478, D.660 Chain C: T.1 Ligands: MN.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.478, A:D.660, H2O.1, H2O.3 MN.5: 5 residues within 4Å: Chain A: K.457, V.685 Chain B: T.1, G.2, A.3 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:V.685, H2O.2, H2O.7

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sheng, G. et al., Structure-based cleavage mechanism of Thermus thermophilus Argonaute DNA guide strand-mediated DNA target cleavage. Proc.Natl.Acad.Sci.USA (2014)

Release Date

2014-01-29

Peptides

Uncharacterized protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Uncharacterized protein

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