SMTL ID : 1ecq.1

E. COLI GLUCARATE DEHYDRATASE BOUND TO 4-DEOXYGLUCARATE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

4 x DXG: 4-DEOXYGLUCARATE(Non-covalent)

DXG.1: 18 residues within 4Å: Chain A: N.27, H.32, T.103, F.104, Y.150, F.152, K.205, K.207, D.235, N.237, E.260, N.289, H.339, S.340, N.341, H.368, R.422 Ligands: MG.2 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:N.27, A:T.103, A:Y.150, A:K.207, A:N.237, A:N.289, A:S.340, A:R.422, A:R.422 Water bridges: A:K.205, A:S.340, A:N.341, A:H.368 Salt bridges: A:H.32, A:K.205, A:K.207, A:H.339, A:H.368, A:R.422 DXG.4: 18 residues within 4Å: Chain B: N.27, H.32, T.103, F.104, Y.150, F.152, K.205, K.207, D.235, N.237, E.260, N.289, H.339, S.340, N.341, H.368, R.422 Ligands: MG.5 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:N.27, B:T.103, B:K.207, B:N.237, B:N.289, B:S.340, B:R.422, B:R.422 Water bridges: B:K.205, B:E.260, B:E.260, B:S.340, B:N.341, B:H.368 Salt bridges: B:H.32, B:K.205, B:K.207, B:K.207, B:H.339, B:H.368, B:R.422 DXG.7: 18 residues within 4Å: Chain C: N.27, H.32, T.103, F.104, Y.150, F.152, K.205, K.207, D.235, N.237, E.260, N.289, H.339, S.340, N.341, H.368, R.422 Ligands: MG.8 18 PLIP interactions: 18 interactions with chain C Hydrogen bonds: C:N.27, C:T.103, C:Y.150, C:K.207, C:N.237, C:N.289, C:S.340, C:R.422, C:R.422 Water bridges: C:S.340, C:N.341, C:H.368 Salt bridges: C:H.32, C:K.205, C:K.207, C:H.339, C:H.368, C:R.422 DXG.10: 19 residues within 4Å: Chain D: N.27, H.32, T.103, F.104, Y.150, F.152, K.205, K.207, D.235, N.237, E.260, N.289, H.339, S.340, N.341, D.366, H.368, R.422 Ligands: MG.11 19 PLIP interactions: 19 interactions with chain D Hydrogen bonds: D:T.103, D:K.207, D:D.235, D:N.237, D:N.289, D:N.341, D:D.366, D:H.368, D:R.422, D:R.422 Water bridges: D:S.340, D:H.368 Salt bridges: D:H.32, D:K.205, D:K.207, D:K.207, D:H.339, D:H.368, D:R.422

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 7 residues within 4Å: Chain A: K.205, K.207, D.235, E.260, N.289, H.339 Ligands: DXG.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.235, A:E.260, H2O.4 MG.5: 6 residues within 4Å: Chain B: K.205, K.207, D.235, E.260, N.289 Ligands: DXG.4 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.235, B:E.260, H2O.13 MG.8: 7 residues within 4Å: Chain C: K.205, K.207, D.235, N.237, E.260, N.289 Ligands: DXG.7 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.235, C:E.260, H2O.19 MG.11: 6 residues within 4Å: Chain D: K.205, D.235, N.237, E.260, N.289 Ligands: DXG.10 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.235, D:E.260, H2O.30

4 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.3: 5 residues within 4Å: Chain A: L.302, F.332 Chain C: G.299, L.302, S.303 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:L.302, A:L.302, A:F.332 Water bridges: A:Q.305 Hydrogen bonds: C:S.303 IPA.6: 5 residues within 4Å: Chain B: G.299, L.302, S.303 Chain D: L.302, F.332 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:G.299 Hydrophobic interactions: D:F.332 IPA.9: 5 residues within 4Å: Chain A: G.299, L.302, S.303 Chain C: L.302, F.332 6 PLIP interactions: 4 interactions with chain C, 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: C:L.302, C:F.332, A:L.302 Water bridges: C:L.302, C:Q.305, B:R.280 IPA.12: 6 residues within 4Å: Chain B: L.302, Q.305, F.332 Chain D: G.299, L.302, S.303 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:Q.305, D:L.302 Water bridges: B:L.302

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gulick, A.M. et al., Evolution of enzymatic activities in the enolase superfamily: crystallographic and mutagenesis studies of the reaction catalyzed by D-glucarate dehydratase from Escherichia coli. Biochemistry (2000)

Release Date

2000-05-23

Peptides

GLUCARATE DEHYDRATASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

GLUCARATE DEHYDRATASE

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