SMTL ID : 2ejt.2 (1 other biounit)

Complex structure of Trm1 from Pyrococcus horikoshii with S-adenosyl-L-Methionine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.1: 18 residues within 4Å: Chain A: F.27, R.36, D.53, L.55, S.56, A.57, I.60, R.61, N.77, D.78, I.79, S.80, D.119, D.120, A.121, D.138, F.140, F.146 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:L.55, A:I.79, A:D.120, A:D.120, A:A.121, A:D.138, A:D.138 Water bridges: A:P.25, A:R.36, A:R.36, A:L.55, A:R.61, A:R.61, A:S.80, A:S.80, A:F.140 Salt bridges: A:R.36, A:R.61 SAM.3: 18 residues within 4Å: Chain B: F.27, R.36, D.53, L.55, S.56, A.57, I.60, R.61, N.77, D.78, I.79, S.80, D.119, D.120, A.121, D.138, F.140, F.146 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:L.55, B:I.79, B:D.120, B:A.121, B:D.138 Water bridges: B:P.25, B:R.36, B:R.36, B:L.55, B:R.61, B:R.61, B:S.80, B:S.80, B:F.140 Salt bridges: B:R.36, B:R.61

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 9 residues within 4Å: Chain A: A.220, L.281, K.282, I.312, E.315, L.316, D.317, H.356, F.357 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.220, A:E.315, A:L.316 Water bridges: A:I.318 GOL.4: 9 residues within 4Å: Chain B: A.220, L.281, K.282, I.312, E.315, L.316, D.317, H.356, F.357 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.220, B:E.315, B:L.316 Water bridges: B:I.318

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ihsanawati et al., Crystal Structure of tRNA N(2),N(2)-Guanosine Dimethyltransferase Trm1 from Pyrococcus horikoshii. J.Mol.Biol. (2008)

Release Date

2007-09-25

Peptides

N(2),N(2)-dimethylguanosine tRNA methyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

N(2),N(2)-dimethylguanosine tRNA methyltransferase

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