SMTL ID : 7tr7.1 (1 other biounit)

APE1 product complex with abasic ssDNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

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

3DR-DC-DG-DA-DT-DG-DC.1: 22 residues within 4Å: Chain A: N.26, E.54, Y.129, N.132, R.135, D.168, N.170, N.180, N.184, N.187, A.188, F.224, T.226, M.228, M.229, A.231, K.234, V.236, W.238, L.240, H.267 Ligands: MG.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.26, A:Y.129, A:Y.129, A:N.132, A:N.170 Salt bridges: A:H.267

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: E.54 Ligands: 3DR-DC-DG-DA-DT-DG-DC.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.54, H2O.1, H2O.2, H2O.3, H2O.7

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hoitsma, N.M. et al., Mechanistic insight into AP-endonuclease 1 cleavage of abasic sites at stalled replication fork mimics. Nucleic Acids Res. (2023)

Release Date

2023-04-12

Peptides

DNA-(apurinic or apyrimidinic site) lyase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA-(apurinic or apyrimidinic site) lyase

Related Entries With Identical Sequence