SMTL ID : 7qbs.1

B12-dependent radical SAM methyltransferase, Mmp10 with [4Fe-4S] cluster, cobalamin, S-adenosyl-L-methionine, and peptide bound.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.33 Å

Oligo State

hetero-1-1-mer

Ligands

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

SF4.1: 12 residues within 4Å: Chain A: P.36, G.37, C.40, G.42, F.43, C.44, C.47, G.113, D.115, S.142, K.144 Ligands: SAM.3 4 PLIP interactions: 4 interactions with chain A, Salt bridges: A:D.115 Metal complexes: A:C.40, A:C.44, A:C.47

1 x FE: FE (III) ION(Non-covalent)

FE.2: 4 residues within 4Å: Chain A: C.60, C.63, C.70, C.73 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.60, A:C.63, A:C.70, A:C.73

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

SAM.3: 17 residues within 4Å: Chain A: Y.46, C.47, Y.48, D.115, Y.140, T.141, S.142, T.166, A.203, V.205, M.234, R.235, F.236, A.237 Chain B: R.7 Ligands: SF4.1, COB.4 13 PLIP interactions: 11 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.140 Hydrogen bonds: A:Y.46, A:Y.48, A:Y.48, A:D.115, A:T.166, A:T.166, A:A.237, A:A.237, B:R.7, B:R.7 pi-Stacking: A:Y.46, A:Y.48

1 x COB: CO-METHYLCOBALAMIN(Non-covalent)

COB.4: 45 residues within 4Å: Chain A: Y.48, F.49, Y.72, V.77, E.79, R.235, A.237, N.242, G.243, L.244, I.245, L.246, N.248, T.282, P.283, F.293, I.314, I.315, T.316, V.319, A.320, D.343, I.344, G.345, C.346, L.347, F.366, I.367, P.368, R.370, F.372, G.394, P.395, E.396, R.397, L.398, S.399, D.401, E.403, M.404 Chain B: A.5, R.6, R.7, A.8 Ligands: SAM.3 32 PLIP interactions: 27 interactions with chain A, 5 interactions with chain B, Hydrophobic interactions: A:Y.48, A:Y.48, A:Y.48, A:L.244, A:I.245, A:V.319, A:I.344, A:F.366, A:P.368, A:F.372, A:L.398, A:L.398, B:R.7 Hydrogen bonds: A:Y.48, A:Y.72, A:V.77, A:R.235, A:L.246, A:N.248, A:D.343, A:D.343, A:D.343, A:G.345, A:R.370, A:L.398, A:S.399, A:S.399, A:D.401, B:R.6, B:A.8 Water bridges: B:R.7, B:R.7

1 x NA: SODIUM ION(Non-functional Binders)

NA.5: 5 residues within 4Å: Chain A: G.143, F.146, D.181, E.183, S.187 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.146, A:S.187

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fyfe, C.D. et al., Crystallographic snapshots of a B 12 -dependent radical SAM methyltransferase. Nature (2022)

Release Date

2022-02-02

Peptides

Methyl coenzyme M reductase-arginine methyltransferase Mmp10: A
Peptide from Methyl-coenzyme M reductase subunit alpha from Methanosarcina acetivorans: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Methyl coenzyme M reductase-arginine methyltransferase Mmp10

Peptide from Methyl-coenzyme M reductase subunit alpha from Methanosarcina acetivorans

Related Entries With Identical Sequence