SMTL ID : 6ca4.2 (2 other biounits)

Crystal structure of humanized D. rerio TDP2 by 14 mutations

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.62 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: D.12, L.14, E.42 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.12, A:E.42, H2O.1, H2O.1, H2O.3

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

EDO.2: 8 residues within 4Å: Chain A: F.89, P.90, T.91, T.92, E.126, K.129, Q.130, V.133 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.91, A:T.91, A:T.92, A:E.126 EDO.3: 10 residues within 4Å: Chain A: L.155, R.156, D.157, R.184, Y.185, L.203, R.204, F.205, R.207 Ligands: MLI.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.155, A:R.204, A:R.207

1 x MLI: MALONATE ION(Non-functional Binders)

MLI.4: 8 residues within 4Å: Chain A: D.157, A.158, W.174, E.175, R.184, R.204, R.207 Ligands: EDO.3 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:A.158, A:E.175 Water bridges: A:E.159, A:V.160, A:R.184, A:R.207, A:R.207, A:R.207 Salt bridges: A:R.204, A:R.207, A:R.207

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ribeiro, C.J.A. et al., New fluorescence-based high-throughput screening assay for small molecule inhibitors of tyrosyl-DNA phosphodiesterase 2 (TDP2). Eur J Pharm Sci (2018)

Release Date

2018-05-02

Peptides

Tyrosyl-DNA phosphodiesterase 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Tyrosyl-DNA phosphodiesterase 2

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