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

Crystal structure of mTREX1-DNA product complex (dNMP)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

1 x DGP: 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE(Non-covalent)

DGP.1: 16 residues within 4Å: Chain A: D.52, L.53, E.54, A.55, G.57, L.58, S.112, G.114, A.115, I.118, T.119, Y.163, H.229, D.234 Ligands: MG.2, MG.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:A.55, A:A.55, A:S.112, A:S.112, A:D.234 Salt bridges: A:H.229

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 9 residues within 4Å: Chain A: D.52, L.53, E.54, H.229, T.230, A.231, D.234 Ligands: DGP.1, MG.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.52, A:E.54, A:D.234 MG.3: 3 residues within 4Å: Chain A: D.52 Ligands: DGP.1, MG.2 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.52, H2O.1, H2O.1, H2O.2, H2O.5 MG.5: 3 residues within 4Å: Chain B: D.52 Ligands: DCM.4, MG.6 5 PLIP interactions: 1 interactions with chain B, 1 Ligand-Ligand interactions, 3 Ligand-Water interactions Metal complexes: B:D.52, DCM.4, H2O.8, H2O.11, H2O.12 MG.6: 9 residues within 4Å: Chain B: D.52, L.53, E.54, H.229, T.230, A.231, D.234 Ligands: DCM.4, MG.5 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:D.52, B:D.52, B:E.54, B:D.234, DCM.4

1 x DCM: 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE(Non-covalent)

DCM.4: 15 residues within 4Å: Chain B: D.52, L.53, E.54, A.55, G.57, L.58, S.112, A.115, I.118, T.119, Y.163, H.229, D.234 Ligands: MG.5, MG.6 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.118 Hydrogen bonds: B:E.54, B:A.55, B:A.55, B:D.234 Water bridges: B:D.52, B:S.112, B:D.234 Salt bridges: B:H.229

1 x CO: COBALT (II) ION(Non-covalent)

CO.7: 4 residues within 4Å: Chain B: K.245, P.246, Q.247, A.248 No protein-ligand interaction detected (PLIP)

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
C

B
E

Three-prime repair exonuclease 1

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