SMTL ID : 6kij.1

Crystal structure of yedK with ssDNA containing an abasic site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.58 Å

Oligo State

monomer

Ligands

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

DT-DT-DC.1: 12 residues within 4Å: Chain A: W.66, W.67, K.69, L.72, N.74, A.75, R.76, S.83, R.84, M.85, F.86 Ligands: PED.2 Protein-ligand interaction information (PLIP) not available

1 x PED: PENTANE-3,4-DIOL-5-PHOSPHATE(Covalent)

PED.2: 9 residues within 4Å: Chain A: C.1, G.2, N.74, R.76, E.104, T.148, H.159, R.161 Ligands: DT-DT-DC.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:C.1, A:C.1, A:D.160 Water bridges: A:R.76, A:R.76 Salt bridges: A:R.76, A:R.161

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 2 residues within 4Å: Chain A: D.20, Y.27 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.20 Water bridges: A:D.20

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, N. et al., Molecular basis of abasic site sensing in single-stranded DNA by the SRAP domain of E. coli yedK. Nucleic Acids Res. (2019)

Release Date

2019-08-07

Peptides

SOS response-associated protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

SOS response-associated protein

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