SMTL ID : 5ej8.1 (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: 34 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, S.32, E.55, T.78, T.81, A.82, N.85, N.117, Q.118 Ligands: MN.2, MG.3, FMT.19 29 PLIP interactions: 22 interactions with chain A, 7 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:S.444, A:N.469, A:Q.473, A:I.474, B:N.117, B:N.117, B:Q.118, B:Q.118 Water bridges: A:V.393, B:A.82, B:A.82 Salt bridges: A:R.395, A:R.413 pi-Stacking: A:F.475 TD6.20: 34 residues within 4Å: Chain A: P.30, G.31, S.32, 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.16, MN.21, MG.22 30 PLIP interactions: 24 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: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:G.472, B:Q.473, B:I.474, A:N.117, A:N.117, A:Q.118, A:Q.118 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: 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.8 MN.21: 8 residues within 4Å: Chain B: D.442, L.443, N.469, G.471, G.472, Q.473 Ligands: TD6.20, MG.22 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.442, B:G.471, H2O.33

4 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

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.8 MG.7: 2 residues within 4Å: Chain A: K.70, D.311 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.311, H2O.1, H2O.5, H2O.9, H2O.17 MG.22: 8 residues within 4Å: Chain B: D.442, L.443, N.469, G.471, G.472, Q.473 Ligands: TD6.20, MN.21 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.442, B:G.471, H2O.33 MG.25: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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:L.454 Water bridges: A:Q.457, B:R.487 GOL.5: 6 residues within 4Å: Chain A: I.361, R.364, H.374, R.375, C.377, D.378 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.364, A:R.364, A:D.378, A:D.378 GOL.23: 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 8 PLIP interactions: 7 interactions with chain B, 1 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

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

EDO.6: 4 residues within 4Å: Chain A: E.16, N.44, S.45, A.46 3 PLIP interactions: 3 interactions with chain A Water bridges: A:E.16, A:S.45, A:S.45 EDO.10: 5 residues within 4Å: Chain A: R.456, Q.457, V.458, S.459, P.528 2 PLIP interactions: 2 interactions with chain A Water bridges: A:V.458, A:P.528 EDO.11: 7 residues within 4Å: Chain A: G.94, L.95, S.128, H.129, P.130, T.131 Chain B: R.121 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:T.131, B:R.121, B:R.121 Water bridges: A:H.129, A:G.163 EDO.12: 7 residues within 4Å: Chain A: Q.383, G.384, P.404, A.405, G.406, Y.407, P.408 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.383 Water bridges: A:Q.383, A:A.405 EDO.13: 9 residues within 4Å: Chain A: S.288, L.289, L.295, P.318, R.413 Chain B: G.115, A.116, N.117 Ligands: EDO.14 7 PLIP interactions: 1 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:N.117, A:S.288, A:S.288 Water bridges: A:S.288, A:S.288, A:L.289, A:L.289 EDO.14: 9 residues within 4Å: Chain A: S.288, L.289, T.290, G.291, L.295, R.395, R.413 Chain B: N.117 Ligands: EDO.13 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.395, A:R.413, A:R.413, B:N.117 Water bridges: A:S.288, A:L.289, A:R.395, A:S.416 EDO.15: 4 residues within 4Å: Chain A: E.207, D.332, E.335, L.336 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.207, A:E.335 Water bridges: A:E.207

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

FMT.8: 6 residues within 4Å: Chain A: A.241, Q.242, W.246, P.247, L.248, P.259 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.242, A:G.245 FMT.9: 9 residues within 4Å: Chain A: K.220, R.221, L.244, G.245, W.246, R.342, Q.343, P.344, W.345 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.246, A:Q.343 FMT.16: 7 residues within 4Å: Chain A: G.31, S.32, R.33, T.78, R.107, Q.118 Ligands: TD6.20 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.32, A:R.33, A:T.78, A:R.107, A:R.107 Water bridges: A:R.33 FMT.17: 8 residues within 4Å: Chain A: A.127, S.128, H.129 Chain B: R.121, Q.122, P.123, G.124, M.125 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.121, A:S.128, A:H.129 FMT.18: 8 residues within 4Å: Chain A: R.121, Q.122, P.123, G.124, M.125 Chain B: A.127, S.128, H.129 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.121, B:S.128, B:S.128, B:H.129 FMT.19: 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:T.78, B:R.107, B:R.107 Water bridges: B:R.33 FMT.24: 3 residues within 4Å: Chain B: N.513, W.514, Q.515 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:W.514, B:Q.515 Water bridges: B:D.365, B:W.514 FMT.26: 8 residues within 4Å: Chain B: A.241, Q.242, G.245, W.246, P.247, L.248, P.259 Ligands: FMT.27 4 PLIP interactions: 4 interactions with chain B Water bridges: B:Q.242, B:Q.242, B:G.245, B:L.248 FMT.27: 6 residues within 4Å: Chain B: P.247, L.260, P.344, C.346, P.350 Ligands: FMT.26 No protein-ligand interaction detected (PLIP) FMT.28: 6 residues within 4Å: Chain B: G.22, R.24, H.25, S.69, Q.71, V.73 1 PLIP interactions: 1 interactions with chain B Water bridges: B:G.22 FMT.29: 4 residues within 4Å: Chain B: E.172, P.173, L.174, Y.175 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.174, B:Y.175 Water bridges: B:E.172, B:E.172 FMT.30: 4 residues within 4Å: Chain B: Q.383, G.433, K.434, P.435 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.433, B:K.434 FMT.31: 7 residues within 4Å: Chain A: N.117 Chain B: L.289, T.290, G.291, L.295, R.395, R.413 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.290, B:R.395, B:R.413, B:R.413 Water bridges: B:R.395, B:S.416

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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