SMTL ID : 8vl7.3 (3 other biounits)

Co-crystal structure of human TREX1 in complex with an inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

homo-dimer

Ligands

2 x 01: (2P)-2-[3-bromo-2-(2-hydroxyethoxy)phenyl]-5-hydroxy-1-methyl-N-(1,2-oxazol-4-yl)-6-oxo-1,6-dihydropyrimidine-4-carboxamide

01.1: 19 residues within 4Å: Chain A: D.17, M.18, E.19, A.20, G.22, L.23, P.28, A.79, A.80, I.83, T.84, Y.128, D.129, L.132, D.199, M.231 Ligands: MG.2, MG.3, PG4.4 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.23, A:I.83 Hydrogen bonds: A:M.18, A:A.20, A:A.20 Water bridges: A:D.199, A:D.199 01.5: 18 residues within 4Å: Chain B: D.17, M.18, E.19, A.20, G.22, L.23, P.28, A.80, I.83, T.84, Y.128, D.129, L.132, H.194, D.199, M.231 Ligands: MG.6, MG.7 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.23, B:I.83 Hydrogen bonds: B:M.18, B:A.20, B:A.20 Water bridges: B:H.194

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.17, E.19, D.199 Ligands: 01.1, MG.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.17, A:E.19, A:D.199, H2O.2 MG.3: 5 residues within 4Å: Chain A: D.17, M.18, D.129 Ligands: 01.1, MG.2 5 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:D.17, A:M.18, A:D.129, H2O.1, 01.1 MG.6: 5 residues within 4Å: Chain B: D.17, E.19, D.199 Ligands: 01.5, MG.7 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.17, B:E.19, B:D.199, H2O.4 MG.7: 5 residues within 4Å: Chain B: D.17, M.18, D.129 Ligands: 01.5, MG.6 5 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: B:D.17, B:M.18, B:D.129, H2O.4, 01.5

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.4: 8 residues within 4Å: Chain A: G.22, L.23, F.25, S.26, S.77, A.79, I.83 Ligands: 01.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.23, A:S.26, A:S.77

1 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.8: 4 residues within 4Å: Chain B: R.210, P.211, Q.212, A.213 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dehghani-Tafti, S. et al., Co-crystal structure of human TREX1 in complex with an inhibitor. To be published

Release Date

2024-01-24

Peptides

Three-prime repair exonuclease 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

Three-prime repair exonuclease 1

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