SMTL ID : 8ftv.1

SgvM methyltransferase triple variant (M144V/F329V/T331A) with SAH and 2-oxo-4-phenylbutanoic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.04 Å

Oligo State

homo-dimer

Ligands

2 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.1: 20 residues within 4Å: Chain A: Y.134, V.137, A.138, S.141, F.149, Y.150, G.169, A.170, G.171, D.192, F.193, A.194, R.219, T.220, I.221, Q.222, G.240, F.241, V.242, D.245 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:S.141, A:G.169, A:G.171, A:F.193, A:I.221, A:Q.222, A:Q.222 Water bridges: A:Y.150, A:Y.150, A:Y.150, A:T.172, A:C.173, A:G.240, A:R.302 pi-Stacking: A:F.193 SAH.4: 20 residues within 4Å: Chain B: Y.134, V.137, A.138, S.141, F.149, Y.150, G.169, A.170, G.171, D.192, F.193, A.194, R.219, T.220, I.221, Q.222, G.240, F.241, V.242, D.245 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:S.141, B:Y.150, B:G.169, B:G.171, B:F.193, B:I.221, B:Q.222, B:Q.222 Water bridges: B:Q.142, B:Y.150, B:Y.150, B:T.172, B:C.173, B:G.240, B:R.302 pi-Stacking: B:F.193

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: F.241, H.244, H.296 Ligands: Y9E.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.244, A:H.296, H2O.3 ZN.5: 4 residues within 4Å: Chain B: F.241, H.244, H.296 Ligands: Y9E.6 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.244, B:H.296, H2O.7

2 x Y9E: 2-oxo-4-phenylbutanoic acid(Non-covalent)

Y9E.3: 11 residues within 4Å: Chain A: W.104, R.132, V.137, S.141, V.144, F.241, H.244, F.288, H.296, V.329 Ligands: ZN.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.104, A:W.104, A:V.144, A:V.144, A:F.241, A:F.241, A:F.288, A:F.288, A:V.329 Water bridges: A:D.245 Salt bridges: A:R.132, A:H.296 Y9E.6: 11 residues within 4Å: Chain B: W.104, R.132, V.137, S.141, V.144, F.241, H.244, F.288, H.296, V.329 Ligands: ZN.5 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:W.104, B:W.104, B:V.144, B:V.144, B:F.241, B:F.241, B:F.288, B:F.288, B:V.329 Water bridges: B:D.245 Salt bridges: B:R.132, B:H.296

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ju, S. et al., A biocatalytic platform for asymmetric alkylation of alpha-keto acids by mining and engineering of methyltransferases. Nat Commun (2023)

Release Date

2023-11-01

Peptides

Methyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Methyltransferase