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

Crystal structure of tRNA wybutosine synthesizing enzyme TYW4

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

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

SAH.1: 22 residues within 4Å: Chain A: I.27, Q.28, T.30, N.31, S.34, K.38, R.88, G.115, C.116, G.117, D.119, D.146, Y.147, L.150, C.195, D.196, L.197, N.198, E.224, V.225, S.226, M.230 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:S.34, A:G.115, A:G.117, A:D.119, A:Y.147, A:Y.147, A:D.196, A:L.197, A:N.198 Water bridges: A:N.198, A:E.224, A:E.224, A:E.224 Salt bridges: A:K.38, A:R.88 pi-Stacking: A:Y.147

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.2: 5 residues within 4Å: Chain A: K.484, S.487, I.524, F.525 Ligands: EDO.3 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.524 Hydrogen bonds: A:K.484, A:F.525, A:F.525 Water bridges: A:S.487 Salt bridges: A:K.484, A:K.484

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

EDO.3: 7 residues within 4Å: Chain A: L.486, S.487, H.488, P.513, L.516, F.525 Ligands: CIT.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.487, A:H.488, A:H.488 Water bridges: A:S.485, A:S.487, A:R.490 EDO.4: 5 residues within 4Å: Chain A: P.264, G.615, T.616, M.654, L.655 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.615, A:L.655 Water bridges: A:F.622 EDO.5: 2 residues within 4Å: Chain A: V.438, D.469 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.440

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Suzuki, Y. et al., Structural basis of tRNA modification with CO2 fixation and methylation by wybutosine synthesizing enzyme TYW4. Nucleic Acids Res. (2009)

Release Date

2009-06-02

Peptides

Leucine carboxyl methyltransferase 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Leucine carboxyl methyltransferase 2

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