SMTL ID : 9ava.2 (5 other biounits)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x K: POTASSIUM ION(Non-covalent)

K.1: 4 residues within 4Å: Chain A: D.15, M.16, E.17, D.197 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.15, A:E.17, A:D.197 K.6: 3 residues within 4Å: Chain B: D.15, E.17, D.197 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.15, B:E.17, B:D.197

2 x 01: (2R)-2-[(5R,6S,8R,9aS)-8-amino-1-oxo-5-(2-phenylethyl)hexahydro-1H-pyrrolo[1,2-a][1,4]diazepin-2(3H)-yl]-N-[(3,4-dichlorophenyl)methyl]-4-methylpentanamide

01.2: 17 residues within 4Å: Chain A: D.15, M.16, E.17, A.18, G.20, L.21, P.26, A.78, I.81, T.82, H.121, N.122, Y.126, D.127, L.130, H.192, M.229 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:A.18, A:L.21, A:P.26, A:I.81, A:I.81, A:T.82, A:N.122, A:Y.126, A:Y.126, A:L.130 Hydrogen bonds: A:D.15 Water bridges: A:H.121, A:N.122, A:H.192 Salt bridges: A:D.15, A:D.127 Halogen bonds: A:A.18 01.7: 16 residues within 4Å: Chain B: D.15, M.16, E.17, A.18, G.20, L.21, P.26, A.78, I.81, T.82, H.121, N.122, Y.126, D.127, L.130, M.229 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:A.18, B:P.26, B:I.81, B:I.81, B:T.82, B:N.122, B:Y.126, B:Y.126, B:L.130 Hydrogen bonds: B:D.15, B:D.15 Water bridges: B:H.121, B:N.122 Salt bridges: B:D.15, B:D.127 Halogen bonds: B:A.18

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

UNX.3: 2 residues within 4Å: Chain A: P.76, A.77 No protein-ligand interaction detected (PLIP) UNX.4: 3 residues within 4Å: Chain A: G.20, L.21, S.75 No protein-ligand interaction detected (PLIP) UNX.5: 2 residues within 4Å: Chain A: P.22, Y.126 No protein-ligand interaction detected (PLIP) UNX.8: 4 residues within 4Å: Chain B: G.20, L.21, S.75 Ligands: UNX.11 No protein-ligand interaction detected (PLIP) UNX.9: 2 residues within 4Å: Chain B: P.76, A.77 No protein-ligand interaction detected (PLIP) UNX.10: 2 residues within 4Å: Chain B: P.22, Y.126 No protein-ligand interaction detected (PLIP) UNX.11: 2 residues within 4Å: Chain B: F.23 Ligands: UNX.8 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

2024-05-15

Peptides

Three-prime repair exonuclease 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
F

Three-prime repair exonuclease 1

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