SMTL ID : 4gek.1

Crystal Structure of wild-type CmoA from E.coli

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: A.83, L.86, R.90, H.115, Y.119 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.90, A:R.90, A:R.90 Salt bridges: A:R.90, A:H.115 SO4.3: 4 residues within 4Å: Chain A: K.186 Chain B: H.239, A.257, E.258 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.258 Salt bridges: B:H.239, A:K.186 SO4.4: 5 residues within 4Å: Chain B: A.83, L.86, R.90, H.115, Y.119 5 PLIP interactions: 5 interactions with chain B Water bridges: B:R.90, B:R.90, B:R.90 Salt bridges: B:R.90, B:H.115

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.2: 22 residues within 4Å: Chain A: F.34, F.42, I.46, Y.53, G.78, C.79, S.80, A.83, D.103, N.104, S.105, M.108, G.130, D.131, I.132, N.146, F.147, T.148, Q.150, F.151, L.152, R.213 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:F.42 Hydrogen bonds: A:G.78, A:S.80, A:N.104, A:N.104, A:D.131, A:I.132, A:N.146, A:Q.150 Water bridges: A:C.79, A:A.83, A:A.84, A:A.84, A:N.146, A:R.213 Salt bridges: A:R.213 GEK.5: 22 residues within 4Å: Chain B: F.34, F.42, Y.53, G.78, C.79, S.80, A.83, D.103, N.104, S.105, M.108, G.130, D.131, I.132, R.133, N.146, F.147, T.148, Q.150, F.151, L.152, R.213 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:F.42 Hydrogen bonds: B:Y.53, B:G.78, B:S.80, B:N.104, B:N.104, B:N.104, B:D.131, B:I.132, B:N.146, B:Q.150 Water bridges: B:C.79, B:A.83, B:A.84, B:A.84, B:N.146, B:R.213 Salt bridges: B:R.213

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, J. et al., Structure-guided discovery of the metabolite carboxy-SAM that modulates tRNA function. Nature (2013)

Release Date

2012-10-10

Peptides

tRNA (cmo5U34)-methyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
G

tRNA (cmo5U34)-methyltransferase