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

Human APE1 product complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.57 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: E.54 Chain B: N.1 Chain C: C.10 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.54, H2O.1, H2O.2, H2O.2

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 10 residues within 4Å: Chain A: V.130, R.143, W.146, D.147, F.150, R.151, L.169, G.197, F.198, L.201 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.151, A:G.197 Water bridges: A:R.143, A:D.147

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

CL.3: 4 residues within 4Å: Chain A: E.59, Y.76, W.77, Y.102 Ligand excluded by PLIP

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

EDO.4: 3 residues within 4Å: Chain A: K.21, E.44, E.45 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.21, A:E.44 Water bridges: A:K.10 EDO.5: 3 residues within 4Å: Chain A: L.2, Y.3, N.235 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.3, A:Y.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Freudenthal, B.D. et al., Capturing snapshots of APE1 processing DNA damage. Nat.Struct.Mol.Biol. (2015)

Release Date

2015-10-14

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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