SMTL ID : 5z2u.2 (1 other biounit)

ThDP-Mn2+ complex of R395A variant of EcMenD soaked with 2-ketoglutarate for 5 min

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-tetramer

Ligands

3 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: 26 residues within 4Å: Chain A: S.391, L.392, R.413, S.416, G.417, I.418, D.419, G.441, D.442, L.443, S.444, Y.447, N.469, G.471, G.472, Q.473, I.474, F.475 Chain B: P.30, E.55, T.78, T.81, A.82, N.117, Q.118 Ligands: MG.2 27 PLIP interactions: 22 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:I.418, A:D.419, A:Y.447, B:P.30, B:T.78 Hydrogen bonds: A:S.391, A:S.391, A:S.391, A:S.391, A:L.392, A:S.416, A:S.416, A:I.418, A:G.441, A:D.442, A:D.442, A:L.443, A:S.444, A:N.469, A:Q.473, A:I.474, B:N.117 Water bridges: A:V.393, A:R.413, B:A.82, B:A.82 Salt bridges: A:R.413 TD6.5: 26 residues within 4Å: Chain A: P.30, E.55, T.78, T.81, A.82, N.117, Q.118 Chain B: N.390, S.391, L.392, R.413, S.416, G.417, I.418, D.419, G.441, D.442, L.443, S.444, Y.447, N.469, G.471, G.472, Q.473, I.474 Ligands: MG.6 27 PLIP interactions: 21 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:I.418, B:D.419, B:Y.447, A:P.30 Hydrogen bonds: B:S.391, B:S.391, B:S.391, B:L.392, B:S.416, B:I.418, B:D.442, B:D.442, B:L.443, B:S.444, B:N.469, B:Q.473, B:I.474, A:N.117 Water bridges: B:V.393, B:G.441, A:S.32, A:A.82, A:A.82, A:Q.118 Salt bridges: B:K.292, B:R.413 pi-Stacking: B:F.475 TD6.10: 27 residues within 4Å: Chain C: N.390, S.391, L.392, R.413, S.416, G.417, I.418, D.419, G.441, D.442, L.443, S.444, Y.447, N.469, G.471, G.472, Q.473, I.474, F.475 Chain D: P.30, E.55, T.78, T.81, A.82, N.117, Q.118 Ligands: MG.11 28 PLIP interactions: 21 interactions with chain C, 7 interactions with chain D Hydrophobic interactions: C:I.418, C:D.419, C:Y.447, D:P.30 Hydrogen bonds: C:S.391, C:S.391, C:S.391, C:L.392, C:S.416, C:I.418, C:G.441, C:D.442, C:D.442, C:L.443, C:S.444, C:N.469, C:Q.473, C:I.474, D:N.117, D:Q.118 Water bridges: C:V.393, C:D.442, D:T.78, D:T.78, D:A.82, D:A.82 Salt bridges: C:R.413 pi-Stacking: C:F.475

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.442, N.469, G.471, G.472 Ligands: TD6.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.442, A:G.471, H2O.3 MG.6: 4 residues within 4Å: Chain B: D.442, N.469, G.471 Ligands: TD6.5 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.442, B:G.471, H2O.22 MG.11: 4 residues within 4Å: Chain C: D.442, N.469, G.471 Ligands: TD6.10 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.442, C:G.471, H2O.37 MG.15: 4 residues within 4Å: Chain D: D.442, N.469, G.471 Ligands: TPP.14 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.442, D:G.471, H2O.52

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: H.49, H.50, T.51, R.430, L.454, Q.457 9 PLIP interactions: 2 interactions with chain B, 7 interactions with chain A Water bridges: B:R.487, B:Q.493, A:H.49, A:T.51, A:Q.457 Hydrogen bonds: A:H.50, A:T.51, A:R.430, A:R.430 GOL.7: 4 residues within 4Å: Chain B: N.470, E.486, N.494, D.539 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.470, B:E.486, B:N.494, B:D.539 GOL.8: 4 residues within 4Å: Chain B: E.16, N.44, S.45, A.46 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:E.16, B:N.44, B:S.45, B:S.45, B:A.46 Water bridges: B:E.16, B:E.16

6 x FMT: FORMIC ACID(Non-functional Binders)

FMT.4: 4 residues within 4Å: Chain A: A.241, Q.242, G.245, W.246 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.242 FMT.9: 3 residues within 4Å: Chain B: H.509, E.516, T.519 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.509, B:A.520 FMT.12: 5 residues within 4Å: Chain C: S.288, L.289, L.295, P.318 Chain D: G.115 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:S.288, C:L.289 Water bridges: D:N.117 FMT.13: 4 residues within 4Å: Chain C: R.363, D.541, T.545, Q.548 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.548, C:Q.548 FMT.17: 5 residues within 4Å: Chain D: E.505, L.506, K.507, T.529, T.530 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.505, D:K.507, D:T.529 FMT.18: 3 residues within 4Å: Chain D: P.173, L.174, Y.175 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:L.174, D:Y.175

1 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.14: 22 residues within 4Å: Chain C: P.30, E.55, T.78, T.81, A.82 Chain D: S.391, L.392, S.416, G.417, I.418, D.419, G.441, D.442, L.443, S.444, Y.447, N.469, G.471, G.472, Q.473, I.474 Ligands: MG.15 22 PLIP interactions: 19 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:I.418, D:D.419, D:Y.447, C:P.30 Hydrogen bonds: D:S.391, D:S.391, D:L.392, D:S.416, D:I.418, D:G.441, D:D.442, D:L.443, D:S.444, D:N.469, D:N.469, D:Q.473, D:I.474 Water bridges: D:V.393, D:S.444, C:A.82, C:A.82 pi-Stacking: D:F.475

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.16: 4 residues within 4Å: Chain D: T.96, E.233, D.310, D.311 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Qin, M.M. et al., Two active site arginines are critical determinants of substrate binding and catalysis in MenD: a thiamine-dependent enzyme in menaquinone biosynthesis. Biochem. J. (2018)

Release Date

2018-11-28

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
E

D
F

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

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