SMTL ID : 7yw2.1

Crystal structure of tRNA 2'-phosphotransferase from Mus musculus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.23 Å

Oligo State

monomer

Ligands

1 x HQG: [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-phosphonooxy-oxolan-2-yl]methyl hydrogen phosphate(Non-covalent)

HQG.1: 21 residues within 4Å: Chain A: R.35, K.79, R.81, H.125, T.127, H.131, S.134, I.135, G.139, L.140, S.141, Q.143, R.145, H.149, S.162, G.163, I.164, R.165 Ligands: GOL.5, GOL.6, GLY.17 26 PLIP interactions: 26 interactions with chain A Hydrogen bonds: A:T.127, A:G.139, A:S.141, A:Q.143, A:S.162, A:G.163, A:G.163 Water bridges: A:Q.99, A:Q.99, A:H.125, A:G.126, A:R.145, A:H.149, A:R.165 Salt bridges: A:R.35, A:R.35, A:K.79, A:K.79, A:R.81, A:H.125, A:R.145, A:R.145, A:R.145, A:R.165, A:R.165, A:R.165

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: R.142, P.197, G.198, N.199, A.200, E.201, G.202 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.142, A:P.197 GOL.5: 5 residues within 4Å: Chain A: F.128, K.130, H.131, R.165 Ligands: HQG.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.130, A:H.131 GOL.6: 5 residues within 4Å: Chain A: S.134, K.138, Q.143, F.203 Ligands: HQG.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.138, A:Q.143 GOL.13: 6 residues within 4Å: Chain A: V.74, N.75, Q.80, F.82, T.83, N.98 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.75, A:F.82, A:N.98 Water bridges: A:F.82, A:L.84

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 6 residues within 4Å: Chain A: K.79, V.160, I.161, S.162, I.164, P.166 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.164 Salt bridges: A:K.79

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

EPE.4: 7 residues within 4Å: Chain A: K.28, S.31, Y.32, R.35, H.36, R.145 Ligands: SOR.14 6 PLIP interactions: 6 interactions with chain A Water bridges: A:R.165, A:R.165, A:R.165 Salt bridges: A:R.35, A:H.36, A:R.145

10 x GLY: GLYCINE(Non-covalent)

GLY.7: 5 residues within 4Å: Chain A: L.39, M.45, R.46, A.47, Q.104 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.104, A:Q.104 GLY.8: 2 residues within 4Å: Chain A: Q.71, L.84 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:Q.71, A:N.75 Water bridges: G.8, G.8 GLY.9: 4 residues within 4Å: Chain A: N.75, T.76, N.77, Q.80 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.75, A:Q.80 GLY.10: 3 residues within 4Å: Chain A: F.128, K.130, N.167 5 PLIP interactions: 1 Ligand-Ligand interactions, 4 interactions with chain A Water bridges: G.10 Hydrogen bonds: A:K.130, A:K.130, A:N.167 Salt bridges: A:R.216 GLY.11: 3 residues within 4Å: Chain A: L.108, E.109, L.110 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.110, A:L.110 GLY.12: 5 residues within 4Å: Chain A: S.152, G.159, C.188, G.192, I.194 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.152, A:G.159 Water bridges: A:S.152 GLY.16: 4 residues within 4Å: Chain A: P.52, Q.54, A.55, Q.58 No protein-ligand interaction detected (PLIP) GLY.17: 4 residues within 4Å: Chain A: K.130, H.131, S.134 Ligands: HQG.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Ligand interactions Water bridges: A:S.134 Salt bridges: A:H.131 Hydrogen bonds: G.17, G.17 GLY.18: 2 residues within 4Å: Chain A: R.142, Q.143 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.141, A:Q.143 Salt bridges: A:R.142 GLY.19: 3 residues within 4Å: Chain A: P.106, H.147, F.187 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Ligand interactions Salt bridges: A:H.147 Hydrogen bonds: G.19, G.19

2 x SOR: sorbitol(Non-covalent)

SOR.14: 6 residues within 4Å: Chain A: H.36, K.40, S.102, G.144, R.145 Ligands: EPE.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.40, A:S.102, A:G.144, A:R.145 Water bridges: A:H.36, A:S.102, A:G.144 SOR.15: 10 residues within 4Å: Chain A: N.23, V.24, S.27, K.28, S.31, V.73, T.76, N.77, E.78, R.81 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.27, A:S.31, A:V.73, A:T.76, A:E.78, A:R.81, A:R.81 Water bridges: A:E.78

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, X. et al., Structural and biochemical insights into the molecular mechanism of TRPT1 for nucleic acid ADP-ribosylation. Nucleic Acids Res. (2023)

Release Date

2023-07-26

Peptides

tRNA 2'-phosphotransferase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

tRNA 2'-phosphotransferase 1