SMTL ID : 7cig.1

Crystal structure of L-methionine decarboxylase Q64A mutant from Streptomyces sp.590 in complexed with L- methionine methyl ester (geminal diamine form).

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-dimer

Ligands

2 x G03: methyl (2S)-2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]-4-methylsulfanyl-butanoate(Covalent)

G03.1: 24 residues within 4Å: Chain A: Y.63, A.64, A.65, G.137, S.138, T.139, N.142, H.195, Y.196, S.197, G.281, T.283, D.336, A.338, S.391, H.393, K.394, S.509 Chain B: N.85, L.87, Y.421, I.422, G.431, S.432 21 PLIP interactions: 17 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:A.338 Hydrogen bonds: A:G.137, A:S.138, A:T.139, A:T.139, A:N.142, A:S.391, A:K.394, B:S.432, B:S.432, B:S.432 Water bridges: A:T.139, A:H.195, A:G.281, A:S.282, B:S.432 Salt bridges: A:H.195, A:H.393, A:K.394, A:K.394 pi-Stacking: A:H.195 G03.2: 23 residues within 4Å: Chain A: N.85, L.87, Y.421, I.422, G.431, S.432 Chain B: Y.63, A.64, A.65, G.137, S.138, T.139, N.142, H.195, Y.196, S.197, G.281, T.283, D.336, A.338, S.391, H.393, K.394 19 PLIP interactions: 14 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:A.338 Hydrogen bonds: B:G.137, B:S.138, B:T.139, B:N.142, B:S.391, A:S.432, A:S.432, A:S.432 Water bridges: B:H.195, B:G.281, B:S.282, A:G.431, A:S.432 Salt bridges: B:H.195, B:H.393, B:K.394, B:K.394 pi-Stacking: B:H.195

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Okawa, A. et al., Structural basis for substrate specificity of l-methionine decarboxylase. Protein Sci. (2021)

Release Date

2021-01-27

Peptides

L-methionine decarboxylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

L-methionine decarboxylase