SMTL ID : 7nto.1

The structure of RRM domain of human TRMT2A at 1.23 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.23 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: R.25, R.29, W.68, K.69 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.22 Water bridges: A:K.69, A:K.69 Salt bridges: A:R.25, A:R.29, A:K.69 SO4.2: 2 residues within 4Å: Chain A: S.4, E.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.4 SO4.3: 2 residues within 4Å: Chain A: H.35, R.51 4 PLIP interactions: 4 interactions with chain A Water bridges: A:E.5, A:H.35 Salt bridges: A:H.35, A:R.51 SO4.4: 3 residues within 4Å: Chain B: H.35, R.51 Ligands: CL.29 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.51 Salt bridges: B:H.35, B:R.51 SO4.16: 4 residues within 4Å: Chain B: R.25, R.29, W.68, K.69 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.22 Water bridges: B:K.69, B:K.69 Salt bridges: B:R.25, B:R.29, B:K.69 SO4.17: 2 residues within 4Å: Chain B: S.4, E.5 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.4 SO4.18: 2 residues within 4Å: Chain B: H.35, R.51 5 PLIP interactions: 5 interactions with chain B Water bridges: B:E.5, B:H.35, B:R.51 Salt bridges: B:H.35, B:R.51 SO4.19: 3 residues within 4Å: Chain A: H.35, R.51 Ligands: CL.14 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Salt bridges: A:H.35, A:R.51 Hydrogen bonds: B:R.51

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

NA.5: 1 residues within 4Å: Chain A: R.24 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.24, A:R.24 NA.6: 4 residues within 4Å: Chain A: S.52, A.53 Ligands: CL.13, CL.30 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Water bridges: B:Q.33, B:E.55 Hydrogen bonds: A:A.53 NA.7: 2 residues within 4Å: Chain A: E.5, K.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.8, A:K.8 Water bridges: A:E.5 NA.8: 2 residues within 4Å: Chain A: L.60, H.64 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.60 NA.9: 3 residues within 4Å: Chain A: R.61 Chain B: R.61 Ligands: NA.24 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.61 NA.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.20: 1 residues within 4Å: Chain B: R.24 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.24, B:R.24 NA.21: 4 residues within 4Å: Chain B: S.52, A.53 Ligands: CL.15, CL.28 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:A.53 Water bridges: A:Q.33 NA.22: 2 residues within 4Å: Chain B: E.5, K.8 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.5, B:K.8 NA.23: 2 residues within 4Å: Chain B: L.60, H.64 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.60 NA.24: 3 residues within 4Å: Chain A: R.61 Chain B: R.61 Ligands: NA.9 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.61 NA.25: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.11: 6 residues within 4Å: Chain A: F.20, R.24, P.34, H.35, K.36, T.37 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.24, A:P.34, A:T.37 EDO.26: 6 residues within 4Å: Chain B: F.20, R.24, P.34, H.35, K.36, T.37 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.24, B:P.34, B:T.37, B:T.37

8 x CL: CHLORIDE ION(Non-functional Binders)

CL.12: 2 residues within 4Å: Chain B: K.58, R.61 Ligand excluded by PLIP CL.13: 6 residues within 4Å: Chain A: R.51, S.52 Chain B: Q.33, E.55 Ligands: NA.6, CL.29 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain A: Q.33 Ligands: SO4.19, CL.28 Ligand excluded by PLIP CL.15: 5 residues within 4Å: Chain A: G.31 Chain B: S.52, A.53, A.54 Ligands: NA.21 Ligand excluded by PLIP CL.27: 2 residues within 4Å: Chain A: K.58, R.61 Ligand excluded by PLIP CL.28: 6 residues within 4Å: Chain A: Q.33, E.55 Chain B: R.51, S.52 Ligands: CL.14, NA.21 Ligand excluded by PLIP CL.29: 3 residues within 4Å: Chain B: Q.33 Ligands: SO4.4, CL.13 Ligand excluded by PLIP CL.30: 5 residues within 4Å: Chain A: S.52, A.53, A.54 Chain B: G.31 Ligands: NA.6 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Margreiter, M.A. et al., Small-molecule modulators of TRMT2A decrease PolyQ aggregation and PolyQ-induced cell death. Comput Struct Biotechnol J (2022)

Release Date

2022-01-19

Peptides

tRNA (uracil-5-)-methyltransferase homolog A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

tRNA (uracil-5-)-methyltransferase homolog A

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