SMTL ID : 1dxf.1

2-dehydro-3-deoxy-galactarate aldolase from Escherichia coli in complex with pyruvate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-hexamer

Ligands

6 x PYR: PYRUVIC ACID(Non-covalent)

PYR.1: 9 residues within 4Å: Chain A: R.75, Q.151, E.153, G.176, P.177, S.178, D.179, L.216 Ligands: MG.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.216 Hydrogen bonds: A:R.75, A:S.178, A:D.179 Water bridges: A:R.75, A:Q.151 PYR.3: 11 residues within 4Å: Chain B: R.75, Q.151, E.153, F.174, G.176, P.177, S.178, D.179, L.216 Chain F: V.123 Ligands: MG.4 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.174, B:L.216 Hydrogen bonds: B:R.75, B:E.153, B:S.178, B:D.179 Water bridges: B:R.75, B:R.75, B:R.75, B:Q.151, B:S.178 PYR.5: 9 residues within 4Å: Chain C: R.75, Q.151, E.153, G.176, P.177, S.178, D.179, L.216 Ligands: MG.6 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:L.216 Hydrogen bonds: C:R.75, C:S.178, C:D.179 Water bridges: C:R.75, C:Q.151 PYR.7: 11 residues within 4Å: Chain B: V.123 Chain D: R.75, Q.151, E.153, F.174, G.176, P.177, S.178, D.179, L.216 Ligands: MG.8 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:F.174, D:L.216 Hydrogen bonds: D:R.75, D:E.153, D:S.178, D:D.179 Water bridges: D:R.75, D:R.75, D:R.75, D:Q.151, D:S.178 PYR.9: 9 residues within 4Å: Chain E: R.75, Q.151, E.153, G.176, P.177, S.178, D.179, L.216 Ligands: MG.10 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:L.216 Hydrogen bonds: E:R.75, E:S.178, E:D.179 Water bridges: E:R.75, E:Q.151 PYR.11: 11 residues within 4Å: Chain D: V.123 Chain F: R.75, Q.151, E.153, F.174, G.176, P.177, S.178, D.179, L.216 Ligands: MG.12 11 PLIP interactions: 11 interactions with chain F Hydrophobic interactions: F:F.174, F:L.216 Hydrogen bonds: F:R.75, F:E.153, F:S.178, F:D.179 Water bridges: F:R.75, F:R.75, F:R.75, F:Q.151, F:S.178

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: Q.151, E.153, D.179 Ligands: PYR.1 5 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: A:E.153, A:D.179, PYR.1, H2O.2, H2O.13 MG.4: 4 residues within 4Å: Chain B: Q.151, E.153, D.179 Ligands: PYR.3 5 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: B:E.153, B:D.179, PYR.3, H2O.6, H2O.27 MG.6: 4 residues within 4Å: Chain C: Q.151, E.153, D.179 Ligands: PYR.5 5 PLIP interactions: 2 interactions with chain C, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: C:E.153, C:D.179, PYR.5, H2O.11, H2O.22 MG.8: 4 residues within 4Å: Chain D: Q.151, E.153, D.179 Ligands: PYR.7 5 PLIP interactions: 2 interactions with chain D, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: D:E.153, D:D.179, PYR.7, H2O.8, H2O.16 MG.10: 4 residues within 4Å: Chain E: Q.151, E.153, D.179 Ligands: PYR.9 5 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: E:E.153, E:D.179, H2O.3, H2O.20, PYR.9 MG.12: 4 residues within 4Å: Chain F: Q.151, E.153, D.179 Ligands: PYR.11 5 PLIP interactions: 2 interactions with chain F, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: F:E.153, F:D.179, PYR.11, H2O.17, H2O.25

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Izard, T. et al., Crystal Structures of the Metal-Dependent 2-Dehydro-3-Deoxy-Galactarate Aldolase Suggest a Novel Reaction Mechanism. Embo J. (2000)

Release Date

2000-08-25

Peptides

2-DEHYDRO-3-DEOXY-GALACTARATE ALDOLASE: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

2-DEHYDRO-3-DEOXY-GALACTARATE ALDOLASE

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