SMTL ID : 2ytz.1 (2 other biounits)

Complex structure of Trm1 from Pyrococcus horikoshii with S-adenosyl-L-Homocystein in the orthorhombic crystal-lattice

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

monomer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: H.129, R.130, R.156 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:H.129, A:R.130, A:R.156 SO4.2: 4 residues within 4Å: Chain A: H.174, P.175, R.176, A.177 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.176, A:A.177 Water bridges: A:R.180 Salt bridges: A:H.174, A:R.176 SO4.3: 4 residues within 4Å: Chain A: K.337, V.338, E.339, R.354 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.338, A:E.339 Salt bridges: A:R.354

1 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.4: 17 residues within 4Å: Chain A: F.27, R.36, D.53, L.55, 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 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:A.57 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:R.36, A:R.36, A:G.59, A:R.61 Salt bridges: A:R.36, A:R.61

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

2007-10-09

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

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

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