SMTL ID : 5z2p.1 (1 other biounit)

ThDP-Mn2+ complex of R413K variant of EcMenD soaked with 2-ketoglutarate for 5 min

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

4 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: 27 residues within 4Å: Chain A: S.391, L.392, R.395, 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, Q.118 Ligands: MN.2, FMT.8, FMT.13 24 PLIP interactions: 21 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:I.418, A:I.418, A:D.419, A:Y.447, B:P.30, B:T.78 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:N.469, A:Q.473, A:I.474, B:Q.118 Water bridges: A:V.393 Salt bridges: A:R.395, A:K.413 pi-Stacking: A:F.475 TD6.9: 27 residues within 4Å: Chain A: P.30, E.55, T.78, T.81, A.82, Q.118 Chain B: N.390, S.391, L.392, R.395, K.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: FMT.7, MN.10 23 PLIP interactions: 3 interactions with chain A, 20 interactions with chain B Hydrophobic interactions: A:P.30, A:T.78, B:I.418, B:D.419, B:Y.447, B:I.474 Water bridges: A:A.82, B:V.393 Hydrogen bonds: B:S.391, B:S.391, B:S.391, B:L.392, B:S.416, B:S.416, B:I.418, B:D.442, B:L.443, B:S.444, B:N.469, B:Q.473, B:I.474 Salt bridges: B:R.395, B:K.413 TD6.14: 27 residues within 4Å: Chain C: N.390, S.391, L.392, R.395, 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 Chain D: P.30, E.55, T.78, T.81, A.82, N.117, Q.118 Ligands: MN.15, FMT.24 27 PLIP interactions: 23 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:I.418, C:D.419, C:Y.447, C:I.474, D:P.30 Hydrogen bonds: C:S.391, C:S.391, C:S.391, C:L.392, C:S.416, C:S.416, C:I.418, 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:R.395, C:R.395, C:N.469, C:N.469, D:A.82 Salt bridges: C:R.395 pi-Stacking: C:F.475 TD6.22: 28 residues within 4Å: Chain C: P.30, E.55, T.78, T.81, A.82, N.117, Q.118 Chain D: N.390, S.391, L.392, R.395, 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.21, MN.23 22 PLIP interactions: 4 interactions with chain C, 18 interactions with chain D Hydrophobic interactions: C:P.30, C:T.78, D:I.418, D:D.419, D:Y.447 Hydrogen bonds: C:N.117, D:S.391, D:S.391, D:S.391, D:L.392, D:S.416, D:S.416, D:I.418, D:D.442, D:L.443, D:S.444, D:N.469, D:Q.473, D:I.474 Water bridges: C:A.82, D:V.393 Salt bridges: D:R.395

4 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.8 MN.10: 4 residues within 4Å: Chain B: D.442, N.469, G.471 Ligands: TD6.9 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.442, B:G.471, H2O.18 MN.15: 4 residues within 4Å: Chain C: D.442, N.469, G.471 Ligands: TD6.14 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.442, C:G.471, H2O.28 MN.23: 4 residues within 4Å: Chain D: D.442, N.469, G.471 Ligands: TD6.22 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.442, D:G.471, H2O.40

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

FMT.3: 4 residues within 4Å: Chain A: I.361, R.364, H.374, D.378 Ligand excluded by PLIP FMT.4: 2 residues within 4Å: Chain A: Q.512, N.513 Ligand excluded by PLIP FMT.5: 2 residues within 4Å: Chain A: K.210, L.336 Ligand excluded by PLIP FMT.6: 3 residues within 4Å: Chain A: R.487 Chain B: I.48, H.49 Ligand excluded by PLIP FMT.7: 7 residues within 4Å: Chain A: G.31, S.32, R.33, T.78, R.107, Q.118 Ligands: TD6.9 Ligand excluded by PLIP FMT.8: 7 residues within 4Å: Chain A: N.390, S.391, V.394, R.395, K.413, S.416 Ligands: TD6.1 Ligand excluded by PLIP FMT.11: 6 residues within 4Å: Chain B: M.1, Q.141, D.180, T.181, G.182, S.184 Ligand excluded by PLIP FMT.12: 4 residues within 4Å: Chain B: K.70, Q.71, P.72, K.99 Ligand excluded by PLIP FMT.13: 7 residues within 4Å: Chain B: G.31, S.32, R.33, T.78, R.107, Q.118 Ligands: TD6.1 Ligand excluded by PLIP FMT.16: 5 residues within 4Å: Chain C: N.494, V.495, H.496 Chain D: M.503, E.505 Ligand excluded by PLIP FMT.17: 5 residues within 4Å: Chain C: E.498, A.501, A.502, L.506, Y.508 Ligand excluded by PLIP FMT.18: 4 residues within 4Å: Chain C: Q.141, G.182, W.185 Ligands: FMT.20 Ligand excluded by PLIP FMT.19: 5 residues within 4Å: Chain C: K.67, R.228, V.409, Y.410, S.411 Ligand excluded by PLIP FMT.20: 3 residues within 4Å: Chain C: T.181, G.182 Ligands: FMT.18 Ligand excluded by PLIP FMT.21: 7 residues within 4Å: Chain C: G.31, S.32, R.33, T.78, R.107, Q.118 Ligands: TD6.22 Ligand excluded by PLIP FMT.24: 7 residues within 4Å: Chain D: G.31, S.32, R.33, T.78, R.107, Q.118 Ligands: TD6.14 Ligand excluded by 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
A

B
B

C
F

D
H

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

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