SMTL ID : 8hcc.1 (1 other biounit)

Crystal structure of mTREX1-RNA product complex (AMP)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.1: 16 residues within 4Å: Chain A: D.52, L.53, E.54, A.55, T.56, G.57, L.58, G.114, A.115, I.118, T.119, Y.163, H.229, D.234 Ligands: MG.2, MG.3 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:A.55, A:A.55, A:Y.163, A:D.234, A:D.234, A:D.234 Water bridges: A:L.53 Salt bridges: A:H.229 AMP.5: 17 residues within 4Å: Chain B: D.52, L.53, E.54, A.55, T.56, G.57, L.58, S.112, G.114, A.115, I.118, T.119, Y.163, H.229, D.234 Ligands: MG.6, MG.7 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:A.55, B:A.55 Water bridges: B:D.52, B:L.53, B:G.114 Salt bridges: B: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: AMP.1, MG.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.52, A:E.54, A:D.234, AMP.1 MG.3: 5 residues within 4Å: Chain A: D.52, L.53, D.164 Ligands: AMP.1, MG.2 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.52, H2O.2, H2O.4, H2O.4, H2O.6 MG.6: 9 residues within 4Å: Chain B: D.52, L.53, E.54, H.229, T.230, A.231, D.234 Ligands: AMP.5, MG.7 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Ligand interactions Metal complexes: B:D.52, B:E.54, B:D.234, AMP.5, AMP.5 MG.7: 5 residues within 4Å: Chain B: D.52, L.53, D.164 Ligands: AMP.5, MG.6 6 PLIP interactions: 1 interactions with chain B, 1 Ligand-Ligand interactions, 4 Ligand-Water interactions Metal complexes: B:D.52, AMP.5, H2O.9, H2O.10, H2O.11, H2O.12

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

NA.4: 5 residues within 4Å: Chain A: I.83, K.245, P.246, Q.247, A.248 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.245, A:Q.247, A:A.248 NA.8: 5 residues within 4Å: Chain B: I.83, K.245, P.246, Q.247, A.248 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.245, B:Q.247, B:A.248 NA.9: 4 residues within 4Å: Chain B: F.134, E.171, R.174, L.175 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.171, B:E.171, B:R.174

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
B

Three-prime repair exonuclease 1

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