SMTL ID : 7u8y.1

TREX1 Structural Studies Capture Small Molecule Inhibition and Implicate Novel DNA Dynamics

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.22 Å

Oligo State

homo-dimer

Ligands

4 x AZN: ALIZARIN RED(Non-covalent)(Covalent)

AZN.1: 9 residues within 4Å: Chain A: A.16, T.17, G.18, L.19, S.73, G.75, A.76, Y.124 Ligands: AZN.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.19 Hydrogen bonds: A:A.16, A:T.17, A:L.19, A:S.73, A:S.73, A:A.76 Water bridges: A:G.75 pi-Stacking: A:Y.124 AZN.2: 13 residues within 4Å: Chain A: D.13, L.14, E.15, G.75, I.79, T.80, H.119, L.174, H.190, D.195 Ligands: AZN.1, MN.3, MN.4 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.79 Hydrogen bonds: A:E.15 Water bridges: A:D.195 pi-Stacking: A:H.190 AZN.5: 13 residues within 4Å: Chain B: D.13, L.14, E.15, G.75, I.79, T.80, H.119, L.174, H.190, D.195 Ligands: AZN.6, MN.7, MN.8 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.79, B:I.79 Hydrogen bonds: B:E.15 Water bridges: B:L.14, B:H.119, B:H.190 Salt bridges: B:H.119 pi-Stacking: B:H.190 AZN.6: 12 residues within 4Å: Chain B: L.14, E.15, A.16, T.17, G.18, L.19, S.73, G.75, A.76, T.80, Y.124 Ligands: AZN.5 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:L.19 Hydrogen bonds: B:A.16, B:A.16, B:A.16, B:T.17, B:L.19, B:S.73, B:S.73, B:G.75, B:A.76 pi-Stacking: B:Y.124

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.3: 3 residues within 4Å: Chain A: D.13 Ligands: AZN.2, MN.4 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.13, H2O.1, H2O.1, H2O.2 MN.4: 6 residues within 4Å: Chain A: D.13, L.14, E.15, D.195 Ligands: AZN.2, MN.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.13, A:E.15, A:D.195 MN.7: 6 residues within 4Å: Chain B: D.13, L.14, E.15, D.195 Ligands: AZN.5, MN.8 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.13, B:E.15, B:D.195 MN.8: 4 residues within 4Å: Chain B: D.13, D.125 Ligands: AZN.5, MN.7 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.13, H2O.3, H2O.3, H2O.4

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hemphill, W.O. et al., TREX1 Structural Studies Capture Small Molecule Inhibition and Implicate Novel DNA Dynamics. to be published

Release Date

2023-03-15

Peptides

Three-prime repair exonuclease 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Three-prime repair exonuclease 1