SMTL ID : 6p93.1

Human APE1 K98A AP-endonuclease product complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: E.54 Chain C: N.1 Chain D: C.10 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.54, A:E.54, H2O.1, H2O.2, H2O.2

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

PEG.2: 9 residues within 4Å: Chain A: R.143, W.146, D.147, F.150, R.151, L.169, G.197, F.198, L.201 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.151, A:G.197

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

CL.3: 6 residues within 4Å: Chain A: E.59, Y.76, W.77, Y.102 Chain B: H.74, R.94 Ligand excluded by PLIP

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

EDO.4: 3 residues within 4Å: Chain A: K.21, E.44, E.45 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.21, A:E.44 Water bridges: A:D.8, A:K.10, A:K.10 EDO.5: 3 residues within 4Å: Chain A: L.2, Y.3, N.235 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.3, A:Y.3, A:R.232 EDO.6: 8 residues within 4Å: Chain B: T.55, C.57, E.59, L.62, W.77, S.78, A.79, V.89 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.55, B:C.57 EDO.7: 7 residues within 4Å: Chain B: R.143, W.146, D.147, F.150, G.197, F.198, L.201 2 PLIP interactions: 2 interactions with chain B Water bridges: B:D.147, B:E.194

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McNeill, D.R. et al., Functions of the major abasic endonuclease (APE1) in cell viability and genotoxin resistance. Mutagenesis (2020)

Release Date

2020-01-01

Peptides

DNA-(apurinic or apyrimidinic site) lyase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

DNA-(apurinic or apyrimidinic site) lyase