SMTL ID : 6nuh.1

Non-covalent DNA-protein complex between E. coli YedK and ssDNA containing an abasic site analog

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.59 Å

Oligo State

monomer

Ligands

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

DG-DT-DC-PDI-DG-DG-DA.1: 27 residues within 4Å: Chain A: C.1, G.2, R.3, A.38, P.39, W.66, W.67, K.69, L.72, I.73, N.74, A.75, R.76, T.79, S.83, R.84, M.85, F.86, W.105, K.112, T.148, H.159, R.161, R.205, G.208, N.209, V.210 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.76, A:R.161

1 x BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

BTB.2: 3 residues within 4Å: Chain A: E.11, D.20, Y.27 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.20 Salt bridges: A:D.20

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thompson, P.S. et al., Protection of abasic sites during DNA replication by a stable thiazolidine protein-DNA cross-link. Nat.Struct.Mol.Biol. (2019)

Release Date

2019-06-26

Peptides

SOS response-associated peptidase YedK: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

SOS response-associated peptidase YedK