SMTL ID : 8hcg.1

Crystal structure of mTREX1-dAMP complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

6 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.1: 13 residues within 4Å: Chain A: L.14, P.15, H.114, N.115, R.118, Y.119, I.146, Y.167, S.168, L.169 Ligands: 1PE.3, D5M.6, MG.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.115, A:N.115 Water bridges: A:H.114 1PE.2: 8 residues within 4Å: Chain A: L.152, A.155, S.156, S.157, P.158, S.159, K.201, A.204 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.156, A:S.156 1PE.3: 10 residues within 4Å: Chain A: N.115, R.118, I.146, K.150, E.153, Q.154, G.160, K.165, Y.167 Ligands: 1PE.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.150, A:G.160, A:Y.167 1PE.9: 13 residues within 4Å: Chain B: L.14, P.15, H.114, N.115, R.118, Y.119, I.146, Y.167, S.168, L.169 Ligands: 1PE.11, D5M.14, MG.15 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.115, B:N.115 Water bridges: B:H.114 1PE.10: 8 residues within 4Å: Chain B: L.152, A.155, S.156, S.157, P.158, S.159, K.201, A.204 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.156, B:S.156 1PE.11: 10 residues within 4Å: Chain B: N.115, R.118, I.146, K.150, E.153, Q.154, G.160, K.165, Y.167 Ligands: 1PE.9 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.150, B:E.153, B:G.160, B:Y.167

4 x NA: SODIUM ION(Non-functional Binders)

NA.4: 3 residues within 4Å: Chain A: R.18, Y.223, G.224 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.18, A:G.224 NA.5: 5 residues within 4Å: Chain A: G.13, L.14, S.17, S.68 Ligands: D5M.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.14, A:S.17, A:S.68 NA.12: 3 residues within 4Å: Chain B: R.18, Y.223, G.224 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.18, B:G.224 NA.13: 5 residues within 4Å: Chain B: G.13, L.14, S.17, S.68 Ligands: D5M.14 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.14, B:S.17, B:S.68

2 x D5M: 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE(Non-covalent)

D5M.6: 18 residues within 4Å: Chain A: D.8, L.9, E.10, A.11, G.13, L.14, S.68, G.70, A.71, I.74, T.75, Y.119, H.185, D.190 Ligands: 1PE.1, NA.5, MG.7, MG.8 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.71 Hydrogen bonds: A:E.10, A:E.10, A:E.10, A:A.11 Salt bridges: A:H.185 D5M.14: 18 residues within 4Å: Chain B: D.8, L.9, E.10, A.11, G.13, L.14, S.68, G.70, A.71, I.74, T.75, Y.119, H.185, D.190 Ligands: 1PE.9, NA.13, MG.15, MG.16 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:A.71 Hydrogen bonds: B:E.10, B:E.10, B:A.11 Salt bridges: B:H.185

4 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 4 residues within 4Å: Chain A: D.8 Ligands: 1PE.1, D5M.6, MG.8 5 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:D.8, H2O.1, H2O.1, H2O.3, D5M.6 MG.8: 9 residues within 4Å: Chain A: D.8, L.9, E.10, H.185, T.186, A.187, D.190 Ligands: D5M.6, MG.7 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Ligand interactions Metal complexes: A:D.8, A:E.10, A:D.190, D5M.6, D5M.6 MG.15: 4 residues within 4Å: Chain B: D.8 Ligands: 1PE.9, D5M.14, MG.16 5 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: B:D.8, H2O.5, H2O.5, H2O.7, D5M.14 MG.16: 9 residues within 4Å: Chain B: D.8, L.9, E.10, H.185, T.186, A.187, D.190 Ligands: D5M.14, MG.15 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.8, B:E.10, B:D.190

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, K.W. et al., Molecular insight into the specific enzymatic properties of TREX1 revealing the diverse functions in processing RNA and DNA/RNA hybrids. Nucleic Acids Res. (2023)

Release Date

2023-11-08

Peptides

Three-prime repair exonuclease 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Three-prime repair exonuclease 1