SMTL ID : 2jla.2 (2 other biounits)

CRYSTAL STRUCTURE OF E.COLI MEND, 2-SUCCINYL-5-ENOLPYRUVYL-6-HYDROXY-3-CYCLOHEXADIENE-1-CARBOXYLATE SYNTHASE - SEMET PROTEIN

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.81 Å

Oligo State

homo-dimer

Ligands

2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.1: 21 residues within 4Å: Chain A: S.393, L.394, S.418, G.419, I.420, D.421, G.443, D.444, L.445, S.446, Y.449, N.471, G.473, G.474, Q.475, I.476 Chain B: P.32, E.57, T.83, A.84 Ligands: MN.2 21 PLIP interactions: 18 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:I.420, A:D.421, B:P.32 Hydrogen bonds: A:S.393, A:S.393, A:L.394, A:S.418, A:I.420, A:D.444, A:L.445, A:S.446, A:N.471, A:Q.475, A:I.476 Water bridges: A:V.395, A:G.443, A:N.471, A:N.471, B:A.84, B:Q.120 pi-Stacking: A:F.477 TPP.7: 25 residues within 4Å: Chain A: P.32, E.57, T.80, T.83, A.84, Q.120 Chain B: S.393, L.394, S.418, G.419, I.420, D.421, G.443, D.444, L.445, S.446, Y.449, N.471, G.473, G.474, Q.475, I.476, F.477 Ligands: CL.3, MN.8 18 PLIP interactions: 16 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.420, B:D.421, B:Y.449, B:F.477, A:P.32, A:T.80 Hydrogen bonds: B:S.393, B:S.393, B:L.394, B:S.418, B:I.420, B:D.444, B:L.445, B:S.446, B:N.471, B:Q.475, B:I.476 pi-Stacking: B:F.477

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

MN.2: 4 residues within 4Å: Chain A: D.444, N.471, G.473 Ligands: TPP.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.444, A:G.473, H2O.86 MN.6: 2 residues within 4Å: Chain A: H.511, D.525 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.511, A:D.525, H2O.87 MN.8: 4 residues within 4Å: Chain B: D.444, N.471, G.473 Ligands: TPP.7 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.444, B:G.473, H2O.198

6 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 6 residues within 4Å: Chain A: G.33, S.34, R.35, T.80, Q.120 Ligands: TPP.7 Ligand excluded by PLIP CL.4: 2 residues within 4Å: Chain A: P.139, R.140 Ligand excluded by PLIP CL.5: 5 residues within 4Å: Chain A: N.392, S.393, R.397, R.415, S.418 Ligand excluded by PLIP CL.9: 5 residues within 4Å: Chain B: G.33, S.34, R.35, T.80, Q.120 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain B: N.392, S.393, R.397, R.415 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain B: T.245, K.343 Ligand excluded by PLIP

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

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

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