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

Crystal structure of Tdp1 catalytic domain in complex with compound XZ520

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.66 Å

Oligo State

monomer

Ligands

1 x K7D: 4-oxo-8-phenyl-1,4-dihydroquinoline-3-carboxylic acid(Non-covalent)

K7D.1: 10 residues within 4Å: Chain A: Y.57, H.116, K.118, N.136, G.311, S.312, P.314, H.346, K.348, W.443 12 PLIP interactions: 12 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 Water bridges: A:K.348, A:K.348 Salt bridges: A:H.116, A:K.118, A:H.346, A:K.348

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

EDO.2: 9 residues within 4Å: Chain A: I.208, G.209, S.210, G.224, T.366, A.368, W.375, L.392, G.393 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.210, A:G.224, A:T.366 EDO.3: 4 residues within 4Å: Chain A: D.175, N.222, W.223, R.227 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.175, A:N.222 Water bridges: A:S.178, A:S.178, A:R.227 EDO.4: 5 residues within 4Å: Chain A: I.158, K.164, S.165, K.173, H.196 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.173 Water bridges: A:K.164, A:K.164, A:S.165, A:H.196

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lountos, G.T. et al., Structure of Tdp1 catalytic domain in complex with compound XZ520. To Be Published

Release Date

2019-11-06

Peptides

Tyrosyl-DNA phosphodiesterase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Tyrosyl-DNA phosphodiesterase 1

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