SMTL ID : 3ps9.1

Crystal structure of MnmC from E. coli

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.54 Å

Oligo State

monomer

Ligands

1 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.1: 36 residues within 4Å: Chain A: I.278, G.279, G.280, G.281, I.282, A.283, Y.301, C.302, A.303, D.304, G.310, A.311, S.312, N.314, G.317, A.318, Y.438, Q.439, L.440, N.469, G.470, Q.472, F.476, G.489, Q.490, V.491, Y.512, G.573, R.575, L.623, G.624, S.625, R.626, G.627, L.628 Ligands: CL.3 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:R.575 Hydrogen bonds: A:G.280, A:A.283, A:A.303, A:D.304, A:D.304, A:A.311, A:S.312, A:S.312, A:A.318, A:A.318, A:L.440, A:L.440, A:N.469, A:Y.512, A:G.624, A:G.627, A:L.628, A:C.629 Water bridges: A:G.280, A:G.281, A:L.309, A:G.310, A:G.310, A:G.310, A:G.470, A:H.471, A:H.471, A:L.623

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

SAM.2: 21 residues within 4Å: Chain A: F.32, Y.36, F.37, E.72, G.74, F.75, G.76, T.77, L.79, N.80, E.109, K.110, F.111, G.163, D.164, I.165, D.186, G.187, F.188, N.193, M.196 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:Y.36, A:G.74, A:G.76, A:T.77, A:L.79, A:N.80, A:K.110, A:F.111, A:D.164, A:I.165, A:D.186 Water bridges: A:Y.36, A:G.78, A:N.80, A:E.109, A:D.186 Salt bridges: A:D.186 pi-Cation interactions: A:F.188

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 4 residues within 4Å: Chain A: N.314, G.317, P.416 Ligands: FAD.1 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, J. et al., Structural basis for hypermodification of the wobble uridine in tRNA by bifunctional enzyme MnmC. Bmc Struct.Biol. (2013)

Release Date

2010-12-22

Peptides

tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein mnmC: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein mnmC