SMTL ID : 8hcf.1

Crystal structure of mTREX1-UMP complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.1: 5 residues within 4Å: Chain A: R.174, K.175, S.176, S.181, R.185 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.174, A:S.176 Salt bridges: A:R.185

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 2 residues within 4Å: Chain A: N.125, R.128 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.125 Water bridges: A:N.125 SO4.3: 7 residues within 4Å: Chain A: A.43, N.46, P.61, R.62, V.63 Chain B: E.91, Q.95 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.46, A:R.62, A:V.63, B:Q.95 SO4.5: 8 residues within 4Å: Chain A: E.91, Q.95 Chain B: A.43, N.46, R.59, P.61, R.62, V.63 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:E.91, A:Q.95, B:N.46, B:R.59, B:R.62, B:V.63 Water bridges: B:P.61

1 x U5P: URIDINE-5'-MONOPHOSPHATE(Non-covalent)

U5P.4: 15 residues within 4Å: Chain B: D.18, L.19, E.20, A.21, T.22, G.23, L.24, S.78, G.80, A.81, I.84, T.85, Y.129, H.195, D.200 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:E.20, B:A.21, B:Y.129 Water bridges: B:D.18, B:L.24, B:S.78, B:D.130, B:D.200 Salt bridges: B:H.195

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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