SMTL ID : 8uv1.2 (1 other biounit)

Structure of TDP1 complexed with compound IB01

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.83 Å

Oligo State

monomer

Ligands

4 x XK6: 8-(fluorosulfonyl)-4-oxo-1,4-dihydroquinoline-3-carboxylic acid

XK6.1: 9 residues within 4Å: Chain A: F.112, T.114, H.116, S.253, P.314, N.369, S.371, W.443 Ligands: XK6.3 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:P.314, A:W.443 Hydrogen bonds: A:S.253, A:N.369 Water bridges: A:H.116, A:H.116, A:N.369 Salt bridges: A:H.116 XK6.2: 2 residues within 4Å: Chain A: G.161, H.163 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.163 pi-Stacking: A:H.163 XK6.3: 12 residues within 4Å: Chain A: Y.57, T.114, H.116, S.252, G.311, S.312, P.314, H.346, K.348, N.369, W.443 Ligands: XK6.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:P.314, A:W.443 Hydrogen bonds: A:H.116, A:S.252, A:N.369 Water bridges: A:N.136, A:K.348 Salt bridges: A:H.346, A:K.348 XK6.4: 4 residues within 4Å: Chain A: G.26, V.27, K.28, P.29 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.29

1 x EDO: 1,2-ETHANEDIOL

EDO.5: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lountos, G.T. et al., Structure of TDP1 complexed with compound IB01. To Be Published

Release Date

2024-09-25

Peptides

Tyrosyl-DNA phosphodiesterase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Tyrosyl-DNA phosphodiesterase 1

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