SMTL ID : 9mnn.1

Crystal structure of L. monocytogenes MenD with Mg2+ and intermediate I bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.79 Å

Oligo State

homo-tetramer

Ligands

4 x TD6: (4S)-4-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3lambda~5~-thiazol-2-yl}-4-hydroxybutanoic acid(Non-covalent)

TD6.1: 27 residues within 4Å: Chain A: N.410, S.411, M.412, P.413, R.415, R.434, N.437, G.438, I.439, D.440, G.461, D.462, L.463, S.464, N.489, G.491, G.492, G.493, I.494, F.495 Chain B: P.34, S.36, E.59, T.82, A.86, Q.122 Ligands: MG.2 23 PLIP interactions: 19 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:I.439, B:P.34, B:T.82 Hydrogen bonds: A:S.411, A:S.411, A:M.412, A:N.437, A:N.437, A:I.439, A:D.462, A:D.462, A:L.463, A:S.464, A:N.489, A:N.489, A:G.493, A:I.494, B:S.36 Water bridges: A:G.461, A:G.461, B:Q.122 Salt bridges: A:R.415, A:R.434 TD6.4: 27 residues within 4Å: Chain A: P.34, S.36, E.59, T.82, A.86, Q.122 Chain B: N.410, S.411, M.412, P.413, R.415, R.434, N.437, G.438, I.439, D.440, G.461, D.462, L.463, S.464, N.489, G.491, G.492, G.493, I.494, F.495 Ligands: MG.5 23 PLIP interactions: 19 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:I.439, A:P.34, A:T.82 Hydrogen bonds: B:S.411, B:S.411, B:M.412, B:N.437, B:N.437, B:I.439, B:D.462, B:D.462, B:L.463, B:S.464, B:N.489, B:N.489, B:G.493, B:I.494, A:S.36 Water bridges: B:G.461, B:G.461, A:Q.122 Salt bridges: B:R.415, B:R.434 TD6.7: 27 residues within 4Å: Chain C: N.410, S.411, M.412, P.413, R.415, R.434, N.437, G.438, I.439, D.440, G.461, D.462, L.463, S.464, N.489, G.491, G.492, G.493, I.494, F.495 Chain D: P.34, S.36, E.59, T.82, A.86, Q.122 Ligands: MG.8 22 PLIP interactions: 18 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:I.439, D:P.34, D:T.82 Hydrogen bonds: C:S.411, C:S.411, C:M.412, C:N.437, C:N.437, C:I.439, C:D.462, C:D.462, C:L.463, C:S.464, C:N.489, C:G.493, C:I.494, D:S.36 Water bridges: C:G.461, C:G.461, D:Q.122 Salt bridges: C:R.415, C:R.434 TD6.10: 27 residues within 4Å: Chain C: P.34, S.36, E.59, T.82, A.86, Q.122 Chain D: N.410, S.411, M.412, P.413, R.415, R.434, N.437, G.438, I.439, D.440, G.461, D.462, L.463, S.464, N.489, G.491, G.492, G.493, I.494, F.495 Ligands: MG.11 22 PLIP interactions: 18 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:I.439, C:P.34, C:T.82 Hydrogen bonds: D:S.411, D:S.411, D:M.412, D:N.437, D:N.437, D:I.439, D:D.462, D:D.462, D:L.463, D:S.464, D:N.489, D:G.493, D:I.494, C:S.36 Water bridges: D:G.461, D:G.461, C:Q.122 Salt bridges: D:R.415, D:R.434

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.462, V.487, N.489, G.491 Ligands: TD6.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.462, A:G.491 MG.3: 2 residues within 4Å: Chain A: A.46, H.48 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:A.46, A:H.48, H2O.1, H2O.1, H2O.2 MG.5: 5 residues within 4Å: Chain B: D.462, V.487, N.489, G.491 Ligands: TD6.4 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.462, B:G.491 MG.6: 2 residues within 4Å: Chain B: A.46, H.48 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:A.46, B:H.48, H2O.1, H2O.2, H2O.3 MG.8: 5 residues within 4Å: Chain C: D.462, V.487, N.489, G.491 Ligands: TD6.7 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.462, C:G.491 MG.9: 2 residues within 4Å: Chain C: A.46, H.48 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:A.46, C:H.48, H2O.3, H2O.4, H2O.4 MG.11: 5 residues within 4Å: Chain D: D.462, V.487, N.489, G.491 Ligands: TD6.10 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.462, D:G.491 MG.12: 2 residues within 4Å: Chain D: A.46, H.48 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:A.46, D:H.48, H2O.3, H2O.4, H2O.5

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bailey, M. et al., Structures of Listeria monocytogenes MenD in ThDP-bound and in-crystallo captured intermediate I-bound forms. Acta Crystallogr.,Sect.F (2025)

Release Date

2025-07-30

Peptides

2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase

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