SMTL ID : 5ej4.1 (3 other biounits)

EcMenD-ThDP-Mn2+ complex soaked with 2-ketoglutarate for 15 min

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

homo-dimer

Ligands

2 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: 31 residues within 4Å: Chain A: N.390, S.391, L.392, R.395, 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, G.31, E.55, T.78, T.81, A.82, N.85, N.117, Q.118 Ligands: MN.2, FMT.6 29 PLIP interactions: 23 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:I.418, A:D.419, A:Y.447, B:P.30 Hydrogen bonds: 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:L.443, A:S.444, A:N.469, A:Q.473, A:I.474, B:N.117, B:N.117 Water bridges: A:V.393, A:N.469, A:N.469, B:T.81, B:T.81, B:R.107 Salt bridges: A:R.395, A:R.413 pi-Stacking: A:F.475 TD6.7: 31 residues within 4Å: Chain A: P.30, G.31, E.55, T.78, T.81, A.82, N.85, N.117, Q.118 Chain B: N.390, S.391, L.392, R.395, 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 Ligands: FMT.5, MN.8 28 PLIP interactions: 23 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:I.418, B:D.419, B:Y.447, A:P.30, A:T.78 Hydrogen bonds: B:S.391, B:S.391, B:S.391, B:L.392, B:S.416, B:S.416, B:I.418, B:G.441, B:D.442, B:L.443, B:S.444, B:N.469, B:Q.473, B:I.474, A:N.117, A:N.117 Water bridges: B:V.393, B:N.469, B:N.469, A:A.82 Salt bridges: B:R.395, B:R.413 pi-Stacking: B:F.475

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 4 residues within 4Å: Chain A: D.442, N.469, G.471 Ligands: TD6.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.442, A:G.471, H2O.7 MN.8: 4 residues within 4Å: Chain B: D.442, N.469, G.471 Ligands: TD6.7 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.442, B:G.471, H2O.24

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: H.49, H.50, T.51, R.430, A.453, L.454, Q.457 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.51, A:T.51, A:R.430, A:R.430, A:L.454 Water bridges: A:H.50, A:Q.457, B:R.487 GOL.4: 6 residues within 4Å: Chain A: I.361, R.364, H.374, R.375, C.377, D.378 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.364, A:H.374 GOL.9: 7 residues within 4Å: Chain B: H.49, H.50, T.51, R.430, A.453, L.454, Q.457 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.51, B:T.51, B:R.430, B:R.430, B:L.454 Water bridges: B:H.50, B:Q.457, A:R.487 GOL.10: 6 residues within 4Å: Chain B: I.361, R.364, H.374, R.375, C.377, D.378 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.364, B:R.364, B:D.378

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

FMT.5: 8 residues within 4Å: Chain A: G.31, S.32, R.33, T.78, S.79, R.107, Q.118 Ligands: TD6.7 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.32, A:R.33, A:R.107, A:R.107, A:Q.118 FMT.6: 7 residues within 4Å: Chain B: G.31, S.32, R.33, T.78, R.107, Q.118 Ligands: TD6.1 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.32, B:R.33, B:R.107, B:R.107, B:Q.118, B:Q.118

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Song, H.G. et al., A Thiamine-Dependent Enzyme Utilizes an Active Tetrahedral Intermediate in Vitamin K Biosynthesis. J.Am.Chem.Soc. (2016)

Release Date

2016-06-01

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

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

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