SMTL ID : 5wn2.1 (1 other biounit)

APE1 exonuclease substrate complex with phosphoglycolate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.29 Å

Oligo State

monomer

Ligands

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

DG-DC-DT-DG-DA-DT-DG-DC-DG.1: 17 residues within 4Å: Chain A: Q.54, K.56, Y.86, Y.129, N.132, R.135 Chain C: C.13, G.14, C.15, A.16, T.17, C.18, A.19, G.20, C.21 Ligands: NA.2, PGA.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.184

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

NA.2: 4 residues within 4Å: Chain A: K.83, Y.86, R.139 Ligands: DG-DC-DT-DG-DA-DT-DG-DC-DG.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.139 NA.7: 2 residues within 4Å: Chain C: G.1, G.2 No protein-ligand interaction detected (PLIP)

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

EDO.3: 2 residues within 4Å: Chain B: C.11 Chain C: G.1 No protein-ligand interaction detected (PLIP)

1 x PGA: 2-PHOSPHOGLYCOLIC ACID(Non-covalent)

PGA.4: 9 residues within 4Å: Chain A: Q.54, Y.129, N.132, N.168, N.170, F.224, L.240, H.267 Ligands: DG-DC-DT-DG-DA-DT-DG-DC-DG.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.26, A:N.132, A:N.168, A:N.170 Water bridges: A:H.267 Salt bridges: A:H.267

2 x CA: CALCIUM ION(Non-functional Binders)

CA.5: 1 residues within 4Å: Chain C: C.21 No protein-ligand interaction detected (PLIP) CA.6: 1 residues within 4Å: Chain C: G.1 No protein-ligand interaction detected (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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