SMTL ID : 6emt.1

Crystal Structure of dual specific Trm10 construct from Thermococcus kodakaraensis.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.79 Å

Oligo State

monomer

Ligands

8 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 4 residues within 4Å: Chain A: P.80, L.81, D.82, R.83 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.82, A:R.83 Salt bridges: A:R.83 ACT.2: 2 residues within 4Å: Chain A: W.23, Y.25 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.23 Water bridges: A:T.85 ACT.3: 2 residues within 4Å: Chain A: D.57, K.181 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Y.58 Salt bridges: A:K.181 ACT.4: 1 residues within 4Å: Chain A: G.88 2 PLIP interactions: 2 interactions with chain A Water bridges: A:W.68, A:G.88 ACT.5: 3 residues within 4Å: Chain A: E.93, K.96, E.97 No protein-ligand interaction detected (PLIP) ACT.6: 3 residues within 4Å: Chain A: R.74, F.77, G.79 No protein-ligand interaction detected (PLIP) ACT.7: 4 residues within 4Å: Chain A: S.62, D.82, I.84, T.85 3 PLIP interactions: 3 interactions with chain A Water bridges: A:S.62, A:T.85, A:T.86 ACT.8: 1 residues within 4Å: Chain A: R.157 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.157 Salt bridges: A:R.155, A:R.157

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 6 residues within 4Å: Chain A: T.85, T.86, Y.87, F.94, E.97, N.98 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.86, A:E.97, A:E.97, A:N.98, A:N.98 Water bridges: A:T.86 GOL.10: 8 residues within 4Å: Chain A: D.29, Y.31, W.68, P.90, T.91, S.92, I.143, L.147 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.91, A:T.91, A:T.91, A:S.92, A:S.92

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.11: 5 residues within 4Å: Chain A: Q.47, Q.50, R.171, N.173, R.174 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.47, A:Q.50, A:R.171, A:N.173, A:N.173, A:R.174

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, R.K. et al., Structural and biochemical analysis of the dual-specificity Trm10 enzyme fromThermococcus kodakaraensisprompts reconsideration of its catalytic mechanism. RNA (2018)

Release Date

2018-06-13

Peptides

tRNA (guanine(9)-/adenine(9)-N1)-methyltransferase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

tRNA (guanine(9)-/adenine(9)-N1)-methyltransferase

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