SMTL ID : 6djh.2 (1 other biounit)

Crystal structure of Tdp1 catalytic domain in complex with compound XZ515

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

monomer

Ligands

1 x GNM: 8-bromo-4-oxo-1,4-dihydroquinoline-3-carboxylic acid(Non-covalent)

GNM.1: 9 residues within 4Å: Chain A: Y.57, H.116, K.118, N.136, G.311, S.312, P.314, H.346, W.443 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.57, A:P.314, A:W.443 Hydrogen bonds: A:Y.57, A:N.136, A:N.136 Salt bridges: A:H.116, A:K.118, A:H.346, A:K.348

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

EDO.2: 8 residues within 4Å: Chain A: I.208, G.209, S.210, T.366, A.368, W.375, L.392, G.393 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.210

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

2019-05-29

Peptides

Tyrosyl-DNA phosphodiesterase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Tyrosyl-DNA phosphodiesterase 1

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