SMTL ID : 7tin.1

The Structure of S. aureus MenD

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-tetramer

Ligands

4 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.1: 23 residues within 4Å: Chain A: S.392, M.393, P.394, N.416, G.417, I.418, D.419, G.439, D.440, L.441, S.442, N.467, G.469, G.470, G.471, I.472, F.473 Chain B: P.33, E.58, T.81, T.84, A.85 Ligands: CA.3 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:I.418, A:I.418, A:F.473 Hydrogen bonds: A:S.392, A:M.393, A:N.416, A:I.418, A:D.440, A:L.441, A:S.442, A:N.467, A:G.471, A:I.472 Water bridges: A:D.440 TPP.5: 22 residues within 4Å: Chain A: P.33, E.58, T.84, A.85 Chain B: S.392, M.393, P.394, N.416, G.417, I.418, D.419, G.439, D.440, L.441, S.442, N.467, G.469, G.470, G.471, I.472, F.473 Ligands: CA.9 21 PLIP interactions: 18 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:I.418, B:I.418, B:F.473, A:P.33 Hydrogen bonds: B:S.392, B:S.392, B:M.393, B:N.416, B:I.418, B:D.440, B:L.441, B:S.442, B:N.467, B:G.471, B:I.472 Water bridges: B:G.439, B:G.439, B:N.467, A:E.58, A:A.85 pi-Stacking: B:F.473 TPP.12: 23 residues within 4Å: Chain C: S.392, M.393, P.394, N.416, G.417, I.418, D.419, G.439, D.440, L.441, S.442, N.467, G.469, G.470, G.471, I.472, F.473 Chain D: P.33, E.58, T.81, T.84, A.85 Ligands: CA.16 16 PLIP interactions: 3 interactions with chain D, 13 interactions with chain C Hydrophobic interactions: D:P.33, C:I.418, C:L.441 Water bridges: D:A.85, D:Q.121 Hydrogen bonds: C:S.392, C:S.392, C:M.393, C:N.416, C:I.418, C:D.440, C:L.441, C:S.442, C:N.467, C:G.471, C:I.472 TPP.18: 23 residues within 4Å: Chain C: P.33, E.58, T.84, A.85 Chain D: S.392, M.393, P.394, N.416, G.417, I.418, D.419, G.439, D.440, L.441, S.442, N.467, G.469, G.470, G.471, I.472, F.473 Ligands: GLY.14, CA.19 19 PLIP interactions: 17 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:I.418, D:I.418, D:F.473, C:P.33 Hydrogen bonds: D:S.392, D:S.392, D:M.393, D:N.416, D:I.418, D:D.440, D:L.441, D:S.442, D:N.467, D:G.469, D:G.471, D:I.472, C:T.84 Water bridges: D:G.439, D:G.439

7 x GLY: GLYCINE(Non-covalent)

GLY.2: 7 residues within 4Å: Chain A: D.109, R.110, L.114, R.115, S.116, A.122, I.123 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:D.109, A:D.109, A:S.116, G.2 Water bridges: A:I.123 Salt bridges: A:R.110 GLY.6: 7 residues within 4Å: Chain B: I.69, E.73, R.100, I.101, P.102, K.168, H.228 4 PLIP interactions: 1 Ligand-Ligand interactions, 3 interactions with chain B Hydrogen bonds: G.6, B:I.69 Salt bridges: B:K.168, B:H.228 GLY.7: 3 residues within 4Å: Chain A: S.35 Chain B: R.396, L.476 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Ligand interactions Water bridges: A:S.35 Hydrogen bonds: G.7, G.7 GLY.8: 4 residues within 4Å: Chain B: R.270, I.472, Y.475, Y.548 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Ligand interactions Salt bridges: B:R.270 Hydrogen bonds: G.8, G.8 GLY.13: 6 residues within 4Å: Chain C: I.69, E.73, I.101, P.102, K.168, H.228 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.73 Salt bridges: C:K.168, C:H.228 GLY.14: 7 residues within 4Å: Chain C: G.34, S.35, R.36, T.81, Q.121 Chain D: F.473 Ligands: TPP.18 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.35, C:R.36, C:Q.121 GLY.15: 6 residues within 4Å: Chain A: N.130 Chain C: N.124, V.126, N.127 Chain D: N.130, N.131 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.124, C:N.127 Water bridges: C:N.131

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: D.440, N.467, G.469 Ligands: TPP.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.440, A:G.469, H2O.2 CA.9: 4 residues within 4Å: Chain B: D.440, N.467, G.469 Ligands: TPP.5 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.440, B:G.469, H2O.3 CA.16: 4 residues within 4Å: Chain C: D.440, N.467, G.469 Ligands: TPP.12 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.440, C:G.469 CA.19: 4 residues within 4Å: Chain D: D.440, N.467, G.469 Ligands: TPP.18 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.440, D:G.469, H2O.9

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

NA.4: 5 residues within 4Å: Chain A: F.44, E.45, A.46, H.47, I.50 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.47 NA.11: 4 residues within 4Å: Chain B: F.44, E.45, H.47, I.50 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.44 NA.17: 5 residues within 4Å: Chain C: F.44, E.45, A.46, H.47, I.50 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:I.50 NA.20: 4 residues within 4Å: Chain D: F.44, E.45, H.47, I.50 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:H.47

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.10: 3 residues within 4Å: Chain B: L.403, N.404, K.405 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stanborough, T. et al., Allosteric inhibition of Staphylococcus aureus MenD by 1,4-dihydroxy naphthoic acid: a feedback inhibition mechanism of the menaquinone biosynthesis pathway. Philos.Trans.R.Soc.Lond.B Biol.Sci. (2023)

Release Date

2022-09-14

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

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