SMTL ID : 2jlc.2 (1 other biounit)

Crystal structure of E.coli MenD, 2-succinyl-5-enolpyruvyl-6-hydroxy- 3-cyclohexadiene-1-carboxylate synthase - native protein

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

4 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.1: 23 residues within 4Å: Chain A: S.412, L.413, S.437, G.438, I.439, D.440, G.462, D.463, L.464, S.465, Y.468, N.490, G.492, G.493, Q.494, I.495, F.496 Chain B: P.51, E.76, T.99, T.102, A.103 Ligands: MN.2 21 PLIP interactions: 18 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:I.439, A:D.440, A:Y.468, B:P.51 Hydrogen bonds: A:S.412, A:S.412, A:L.413, A:S.437, A:I.439, A:D.463, A:L.464, A:S.465, A:N.490, A:Q.494, A:I.495 Water bridges: A:V.414, A:N.490, A:N.490, B:A.103, B:A.103 pi-Stacking: A:F.496 TPP.3: 24 residues within 4Å: Chain A: P.51, E.76, T.99, T.102, A.103, Q.139 Chain B: S.412, L.413, S.437, G.438, I.439, D.440, G.462, D.463, L.464, S.465, Y.468, N.490, G.492, G.493, Q.494, I.495, F.496 Ligands: MN.4 23 PLIP interactions: 20 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:I.439, B:D.440, B:Y.468, B:I.495, B:F.496, A:P.51 Hydrogen bonds: B:S.412, B:L.413, B:S.437, B:I.439, B:G.462, B:D.463, B:L.464, B:S.465, B:N.490, B:Q.494, B:I.495 Water bridges: B:V.414, B:N.490, B:N.490, A:A.103, A:A.103 pi-Stacking: B:F.496 TPP.5: 23 residues within 4Å: Chain C: S.412, L.413, S.437, G.438, I.439, D.440, G.462, D.463, L.464, S.465, Y.468, N.490, G.492, G.493, Q.494, I.495, F.496 Chain D: P.51, E.76, T.99, T.102, A.103 Ligands: MN.6 21 PLIP interactions: 18 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:I.439, C:D.440, C:Y.468, D:P.51 Hydrogen bonds: C:S.412, C:S.412, C:L.413, C:S.437, C:I.439, C:D.463, C:L.464, C:S.465, C:N.490, C:Q.494, C:I.495 Water bridges: C:V.414, C:N.490, C:N.490, D:A.103, D:A.103 pi-Stacking: C:F.496 TPP.7: 24 residues within 4Å: Chain C: P.51, E.76, T.99, T.102, A.103, Q.139 Chain D: S.412, L.413, S.437, G.438, I.439, D.440, G.462, D.463, L.464, S.465, Y.468, N.490, G.492, G.493, Q.494, I.495, F.496 Ligands: MN.8 23 PLIP interactions: 20 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:I.439, D:D.440, D:Y.468, D:I.495, D:F.496, C:P.51 Hydrogen bonds: D:S.412, D:L.413, D:S.437, D:I.439, D:G.462, D:D.463, D:L.464, D:S.465, D:N.490, D:Q.494, D:I.495 Water bridges: D:V.414, D:N.490, D:N.490, C:A.103, C:A.103 pi-Stacking: D:F.496

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

MN.2: 4 residues within 4Å: Chain A: D.463, N.490, G.492 Ligands: TPP.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.463, A:G.492, H2O.5 MN.4: 4 residues within 4Å: Chain B: D.463, N.490, G.492 Ligands: TPP.3 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.463, B:G.492, H2O.10 MN.6: 4 residues within 4Å: Chain C: D.463, N.490, G.492 Ligands: TPP.5 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.463, C:G.492, H2O.14 MN.8: 4 residues within 4Å: Chain D: D.463, N.490, G.492 Ligands: TPP.7 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.463, D:G.492, H2O.19

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dawson, A. et al., Specificity and Reactivity in Menaquinone Biosynthesis: The Structure of Escherichia Coli Mend (2-Succinyl-5-Enolpyruvyl-6-Hydroxy-3-Cyclohexadiene-1-Carboxylate Synthase). J.Mol.Biol. (2008)

Release Date

2008-10-21

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
A

D
B

2-SUCCINYL-5-ENOLPYRUVYL-6-HYDROXY-3-CYCLOHEXENE -1-CARBOXYLATE SYNTHASE

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