SMTL ID : 7kb1.1

Complex of O-acety-L-homoserine aminocarboxypropyltransferase (MetY) from Thermotoga maritima and a key reaction intermediate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-tetramer

Ligands

3 x WBJ: (2E)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)imino]but-3-enoic acid(Non-covalent)

WBJ.1: 20 residues within 4Å: Chain A: S.87, G.88, Q.89, I.92, Y.113, E.157, N.161, D.186, T.188, S.207, T.209, K.210, G.220, A.369, N.370, I.371, T.385, R.405 Chain B: Y.58, R.60 17 PLIP interactions: 14 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:Y.113, A:Y.113, A:T.188, B:Y.58 Hydrogen bonds: A:G.88, A:Q.89, A:N.161, A:S.207, A:S.207, A:S.207, A:K.210, B:Y.58 Water bridges: A:T.116 Salt bridges: A:K.210, A:K.210, A:R.405, B:R.60 WBJ.3: 19 residues within 4Å: Chain A: Y.58, R.60 Chain B: S.87, G.88, Q.89, I.92, Y.113, E.157, N.161, D.186, T.188, S.207, T.209, K.210, G.220, A.369, N.370, I.371, R.405 17 PLIP interactions: 14 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:Y.113, B:Y.113, A:Y.58 Hydrogen bonds: B:G.88, B:Q.89, B:N.161, B:S.207, B:S.207, B:S.207, B:T.209, B:K.210, A:Y.58 Water bridges: B:T.116 Salt bridges: B:K.210, B:K.210, B:R.405, A:R.60 WBJ.5: 20 residues within 4Å: Chain C: S.87, G.88, Q.89, I.92, Y.113, E.157, N.161, D.186, T.188, S.207, T.209, K.210, I.219, G.220, N.370, I.371, T.385, R.405 Chain D: Y.58, R.60 14 PLIP interactions: 2 interactions with chain D, 12 interactions with chain C Hydrophobic interactions: D:Y.58, C:Y.113, C:Y.113, C:T.188 Salt bridges: D:R.60, C:K.210, C:K.210, C:R.405 Hydrogen bonds: C:G.88, C:Q.89, C:N.161, C:T.188, C:S.207, C:K.210

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

NA.2: 1 residues within 4Å: Chain A: E.52 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.52

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.4: 5 residues within 4Å: Chain B: L.48, L.51, E.53, P.54, F.255 1 PLIP interactions: 1 interactions with chain B Water bridges: B:G.55

1 x PLP: PYRIDOXAL-5'-PHOSPHATE(Non-covalent)

PLP.6: 15 residues within 4Å: Chain C: Y.58, R.60 Chain D: S.87, G.88, Q.89, I.92, Y.113, N.161, D.186, T.188, S.207, T.209, K.210, G.220, I.371 15 PLIP interactions: 13 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:Y.113, D:T.188 Hydrogen bonds: D:S.87, D:G.88, D:Q.89, D:N.161, D:T.188, D:S.207, D:T.209, D:K.210, C:Y.58 Water bridges: D:Y.113, D:E.157 Salt bridges: D:K.210, C:R.60

1 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 2 residues within 4Å: Chain D: I.147, H.179 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:H.179

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brewster, J.L. et al., Structures and kinetics of Thermotoga maritima MetY reveal new insights into the predominant sulfurylation enzyme of bacterial methionine biosynthesis. J.Biol.Chem. (2021)

Release Date

2021-06-23

Peptides

O-acetyl-L-homoserine sulfhydrylase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

O-acetyl-L-homoserine sulfhydrylase

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