SMTL ID : 5ej8.3 (3 other biounits)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.34 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: 33 residues within 4Å: Chain A: N.390, S.391, L.392, V.393, 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, MG.3, FMT.14 29 PLIP interactions: 24 interactions with chain A, 5 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:L.392, A:S.416, A:S.416, A:I.418, A:G.441, A:D.442, A:L.443, A:S.444, A:S.444, A:N.469, A:G.472, A:Q.473, A:I.474, B:N.117, B:N.117 Water bridges: A:V.393, A:N.469, A:N.469, B:A.82, B:A.82 Salt bridges: A:R.395, A:R.413 pi-Stacking: A:F.475 TD6.15: 33 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, V.393, 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.13, MN.16, MG.17 30 PLIP interactions: 25 interactions with chain B, 5 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:L.392, B:S.416, B:S.416, B:I.418, B:G.441, B:D.442, B:L.443, B:S.444, B:S.444, B:N.469, B:N.469, B:G.472, 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, A:Q.118 Salt bridges: B:R.395, B:R.413 pi-Stacking: B:F.475

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

MN.2: 8 residues within 4Å: Chain A: D.442, L.443, N.469, G.471, G.472, Q.473 Ligands: TD6.1, MG.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.442, A:G.471, H2O.4 MN.16: 8 residues within 4Å: Chain B: D.442, L.443, N.469, G.471, G.472, Q.473 Ligands: TD6.15, MG.17 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.442, B:G.471, H2O.34

3 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 9 residues within 4Å: Chain A: G.441, D.442, L.443, N.469, G.471, G.472, Q.473 Ligands: TD6.1, MN.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.442, A:G.471, H2O.4 MG.7: 2 residues within 4Å: Chain A: K.70, D.311 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.311, H2O.1, H2O.2, H2O.6, H2O.9, H2O.9 MG.17: 8 residues within 4Å: Chain B: D.442, L.443, N.469, G.471, G.472, Q.473 Ligands: TD6.15, MN.16 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.442, B:G.471, H2O.34

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 10 residues within 4Å: Chain A: H.49, H.50, T.51, H.52, L.61, R.430, A.453, L.454, Q.457 Chain B: R.487 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.49, A:T.51, A:T.51, A:R.430, A:R.430, A:Q.457 Water bridges: A:Q.457, B:R.487 GOL.18: 10 residues within 4Å: Chain A: R.487 Chain B: H.49, H.50, T.51, H.52, L.61, R.430, A.453, L.454, Q.457 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:H.49, B:T.51, B:T.51, B:R.430, B:R.430, B:L.454 Water bridges: B:Q.457, A:R.487, A:R.487 GOL.19: 6 residues within 4Å: Chain B: I.361, R.364, H.374, R.375, C.377, D.378 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.364, B:R.364, B:D.378, B:D.378, B:D.378

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

FMT.5: 8 residues within 4Å: Chain A: P.123, G.124, S.133, I.134, S.135, H.165, I.166, N.167 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.124, A:I.134, A:I.134, A:H.165, A:N.167 FMT.6: 4 residues within 4Å: Chain A: E.172, P.173, L.174, Y.175 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.174, A:Y.175 FMT.8: 2 residues within 4Å: Chain A: K.70, S.230 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.70 Water bridges: A:S.230, A:S.230 FMT.9: 7 residues within 4Å: Chain A: R.121, P.123, G.124, M.125 Chain B: A.127, S.128, H.129 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.128, B:S.128, B:H.129 FMT.10: 7 residues within 4Å: Chain A: S.288, L.289, L.295, P.318 Chain B: G.115, A.116, N.117 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:N.117 Water bridges: A:S.288, A:S.288, A:L.289 FMT.11: 5 residues within 4Å: Chain A: R.24, H.25, I.48, S.69, A.431 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.25 FMT.13: 7 residues within 4Å: Chain A: G.31, S.32, R.33, T.78, R.107, Q.118 Ligands: TD6.15 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.32, A:R.33, A:T.78, A:R.107, A:R.107, A:Q.118 Water bridges: A:S.32, A:R.33, A:Q.118 FMT.14: 7 residues within 4Å: Chain B: G.31, S.32, R.33, T.78, R.107, Q.118 Ligands: TD6.1 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:S.32, B:R.33, B:T.78, B:R.107, B:R.107, B:Q.118 Water bridges: B:S.32, B:R.33, B:Q.118 FMT.20: 3 residues within 4Å: Chain B: K.197, P.198, R.201 No protein-ligand interaction detected (PLIP) FMT.21: 6 residues within 4Å: Chain B: A.241, Q.242, W.246, P.247, L.248, P.259 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:W.246 Water bridges: B:Q.242, B:Q.242, B:G.245 FMT.24: 7 residues within 4Å: Chain A: G.115, A.116, N.117 Chain B: S.288, L.289, L.295, P.318 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:L.289, A:N.117 Water bridges: B:S.288

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

EDO.12: 9 residues within 4Å: Chain A: G.245, W.246, P.247, L.248, P.259, L.260, P.344, C.346, P.350 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.245 Water bridges: A:G.245 EDO.22: 5 residues within 4Å: Chain B: L.183, Q.186, Q.187, W.193, Q.194 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Q.187 EDO.23: 4 residues within 4Å: Chain A: R.487 Chain B: F.47, I.48, H.49 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.487, B:H.49, B:H.49

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
E

B
F

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

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