SMTL ID : 6mj5.1 (1 other biounit)

Crystal structure of Tdp1 catalytic domain in complex with compound XZ519

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: D.174, N.221, W.222, R.226 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.174, A:N.221 Water bridges: A:S.177 EDO.2: 8 residues within 4Å: Chain A: I.207, G.208, S.209, T.365, A.367, W.374, L.391, G.392 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.209 EDO.3: 8 residues within 4Å: Chain A: T.336, V.407, K.408, Q.409, V.424, Y.426, D.427, L.428 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.424, A:L.428, A:L.428 Water bridges: A:D.427

1 x JTA: 4-hydroxy-8-nitroquinoline-3-carboxylic acid(Non-covalent)

JTA.4: 9 residues within 4Å: Chain A: Y.56, H.115, K.117, N.135, G.310, S.311, P.313, H.345, W.442 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.56, A:P.313, A:P.313, A:W.442 Hydrogen bonds: A:N.135 Water bridges: A:H.115, A:K.117, A:D.140, A:S.311, A:K.347 Salt bridges: A:H.115, A:K.117, A:H.345, A:K.347

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lountos, G.T. et al., Identification of a ligand binding hot spot and structural motifs replicating aspects of tyrosyl-DNA phosphodiesterase I (TDP1) phosphoryl recognition by crystallographic fragment cocktail screening. Nucleic Acids Res. (2019)

Release Date

2019-07-03

Peptides

Tyrosyl-DNA phosphodiesterase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Tyrosyl-DNA phosphodiesterase 1

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