SMTL ID : 9ccb.1

X-ray crystal structure of methyl-coenzyme M reductase glutamine methylase (MgmA) from Methanothermobacter marburgensis with hydroxycobalamin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.08 Å

Oligo State

monomer

Ligands

1 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.1: 8 residues within 4Å: Chain A: C.185, C.189, C.192, P.195, G.230, T.231, D.268, R.270 7 PLIP interactions: 7 interactions with chain A, Salt bridges: A:D.268, A:D.268, A:D.268 Metal complexes: A:C.185, A:C.189, A:C.192, A:D.268

1 x B12: COBALAMIN(Non-covalent)

B12.2: 34 residues within 4Å: Chain A: E.30, T.33, Y.34, G.35, I.39, F.65, I.66, S.67, Q.69, S.70, T.71, H.73, V.89, G.91, G.92, P.93, I.111, G.113, E.114, G.115, E.116, Y.178, E.180, R.183, F.191, C.192, Q.193, V.194, F.197, F.198, S.228, E.365, I.367, H.438 27 PLIP interactions: 27 interactions with chain A, Hydrophobic interactions: A:T.33, A:Y.34, A:I.39, A:F.65, A:P.93, A:I.111, A:Y.178, A:Q.193, A:V.194, A:I.367 Hydrogen bonds: A:E.30, A:E.30, A:G.35, A:S.70, A:T.71, A:T.71, A:G.92, A:G.115, A:E.116, A:Q.193, A:Q.193, A:E.365 Water bridges: A:Y.34, A:Y.34, A:Y.34, A:S.228, A:S.228

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 2 residues within 4Å: Chain A: E.254, E.257 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.254, A:E.254, A:E.257 CA.4: 2 residues within 4Å: Chain A: E.316, E.319 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.316, A:E.319, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rodriguez Carrero, R.J. et al., Genetic and biochemical characterization of a radical SAM enzyme required for post-translational glutamine methylation of methyl-coenzyme M reductase. Mbio (2025)

Release Date

2025-01-01

Peptides

Radical SAM core domain-containing protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Radical SAM core domain-containing protein