SMTL ID : 4iwn.1

Crystal structure of a putative methyltransferase CmoA in complex with a novel SAM derivative

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

homo-dimer

Ligands

2 x GEK: (2S)-4-[{[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}(carboxylatomethyl)sulfonio] -2-ammoniobutanoate(Non-covalent)

GEK.1: 21 residues within 4Å: Chain A: F.10, Y.21, I.25, G.46, C.47, S.48, A.51, D.71, N.72, S.73, M.76, G.98, D.99, I.100, R.101, N.114, F.115, T.116, F.119, L.120, R.181 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:F.10 Hydrogen bonds: A:G.46, A:S.48, A:N.72, A:N.72, A:D.99, A:I.100, A:N.114 Water bridges: A:C.47, A:A.51, A:A.52, A:A.52, A:N.72, A:N.72, A:R.101, A:N.114 Salt bridges: A:R.181 GEK.3: 21 residues within 4Å: Chain B: F.10, Y.21, I.25, G.46, C.47, S.48, A.51, D.71, N.72, S.73, M.76, G.98, D.99, I.100, R.101, N.114, F.115, T.116, F.119, L.120, R.181 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:F.10 Hydrogen bonds: B:Y.21, B:G.46, B:S.48, B:N.72, B:N.72, B:S.73, B:D.99, B:I.100, B:N.114, B:Q.118 Water bridges: B:C.47, B:A.51, B:A.52, B:A.52, B:R.101, B:N.114 Salt bridges: B:R.181

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.2: 8 residues within 4Å: Chain A: N.23, S.26, M.27, M.30 Chain B: G.20, N.23, F.166, F.215 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:N.23, B:F.166, B:F.166, B:F.215 Water bridges: A:S.26 Hydrogen bonds: B:G.20 MPD.4: 7 residues within 4Å: Chain A: G.20, N.23, F.166, C.214, F.215 Chain B: N.23, S.26 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.166, A:F.215 Water bridges: A:G.20

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Byrne, R.T. et al., S-Adenosyl-S-carboxymethyl-L-homocysteine: a novel cofactor found in the putative tRNA-modifying enzyme CmoA. Acta Crystallogr.,Sect.D (2013)

Release Date

2013-05-29

Peptides

tRNA (cmo5U34)-methyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

tRNA (cmo5U34)-methyltransferase