SMTL ID : 9e9b.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.61 Å

Oligo State

homo-tetramer

Ligands

4 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.1: 24 residues within 4Å: Chain A: S.411, M.412, P.413, 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, E.59, T.82, T.85, A.86, Q.122 Ligands: MG.2 18 PLIP interactions: 16 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.439, A:D.440, A:F.495, B:P.34 Hydrogen bonds: A:S.411, A:S.411, A:M.412, A:N.437, A:I.439, A:G.461, A:D.462, A:L.463, A:S.464, A:N.489, A:G.493, A:I.494 Water bridges: A:S.464, B:A.86 TPP.3: 24 residues within 4Å: Chain A: P.34, E.59, T.82, T.85, A.86, Q.122 Chain B: S.411, M.412, P.413, 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.4 18 PLIP interactions: 16 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.439, B:D.440, B:F.495, A:P.34 Hydrogen bonds: B:S.411, B:S.411, B:M.412, B:N.437, B:I.439, B:G.461, B:D.462, B:L.463, B:S.464, B:N.489, B:G.493, B:I.494 Water bridges: B:S.464, A:A.86 TPP.5: 24 residues within 4Å: Chain C: S.411, M.412, P.413, 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, E.59, T.82, T.85, A.86, Q.122 Ligands: MG.6 20 PLIP interactions: 17 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:I.439, C:D.440, C:F.495, D:P.34 Hydrogen bonds: C:S.411, C:S.411, C:M.412, C:N.437, C:I.439, C:G.461, C:D.462, C:L.463, C:S.464, C:N.489, C:N.489, C:G.493, C:I.494 Water bridges: C:S.464, D:T.85, D:A.86 TPP.7: 24 residues within 4Å: Chain C: P.34, E.59, T.82, T.85, A.86, Q.122 Chain D: S.411, M.412, P.413, 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.8 20 PLIP interactions: 17 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:I.439, D:D.440, D:F.495, C:P.34 Hydrogen bonds: D:S.411, D:S.411, D:M.412, D:N.437, D:I.439, D:G.461, D:D.462, D:L.463, D:S.464, D:N.489, D:N.489, D:G.493, D:I.494 Water bridges: D:S.464, C:T.85, C:A.86

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.462, V.487, N.489, G.491 Ligands: TPP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.462, A:G.491 MG.4: 5 residues within 4Å: Chain B: D.462, V.487, N.489, G.491 Ligands: TPP.3 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.462, B:G.491 MG.6: 5 residues within 4Å: Chain C: D.462, V.487, N.489, G.491 Ligands: TPP.5 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.462, C:G.491 MG.8: 5 residues within 4Å: Chain D: D.462, V.487, N.489, G.491 Ligands: TPP.7 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.462, D:G.491

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

Related Entries With Identical Sequence