SMTL ID : 5wn3.2 (1 other biounit)

APE1 F266A exonuclease substrate complex with a C/T mismatch

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 6 residues within 4Å: Chain A: K.10, A.18, T.19, K.21, D.48, Y.273 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.48 Water bridges: A:K.10 EDO.2: 5 residues within 4Å: Chain A: L.2, Y.3, W.225, R.232, N.235 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.3, A:Y.3, A:R.232

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

NA.3: 7 residues within 4Å: Chain A: S.24, W.25, N.26, Q.53, G.167, D.168, D.241 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.24, A:N.26, A:Q.53, A:D.241

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 2 residues within 4Å: Chain A: F.120, D.121 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain A: Y.215, P.216, N.217, T.218 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Whitaker, A.M. et al., Molecular snapshots of APE1 proofreading mismatches and removing DNA damage. Nat Commun (2018)

Release Date

2018-02-28

Peptides

DNA-(apurinic or apyrimidinic site) lyase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA-(apurinic or apyrimidinic site) lyase

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