SMTL ID : 1dxe.1

2-dehydro-3-deoxy-galactarate aldolase from Escherichia coli

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-hexamer

Ligands

12 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 11 residues within 4Å: Chain A: W.24, R.75, Q.151, E.153, F.174, G.176, P.177, S.178, L.216 Ligands: PO4.2, MG.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.151, A:S.178 Water bridges: A:R.75, A:R.75 Salt bridges: A:R.75 PO4.2: 6 residues within 4Å: Chain A: W.24, R.75, L.216 Chain C: S.124, V.125 Ligands: PO4.1 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain C Hydrogen bonds: A:W.24, A:R.75, C:V.125 Water bridges: A:S.238, A:S.238, A:S.238, A:S.238, C:S.124, C:S.126, C:S.126 PO4.4: 11 residues within 4Å: Chain B: W.24, R.75, Q.151, E.153, F.174, G.176, P.177, S.178, L.216 Ligands: PO4.5, MG.6 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain F Hydrogen bonds: B:E.153, B:S.178 Water bridges: B:R.75, B:Q.151, B:E.153, F:V.123 Salt bridges: B:R.75 PO4.5: 6 residues within 4Å: Chain B: W.24, R.75, L.216 Chain F: S.124, V.125 Ligands: PO4.4 11 PLIP interactions: 5 interactions with chain B, 6 interactions with chain F Hydrogen bonds: B:R.75, F:S.124, F:S.124, F:V.125 Water bridges: B:D.47, B:S.238, B:S.238, B:S.238, F:S.124, F:S.126, F:S.126 PO4.7: 11 residues within 4Å: Chain C: W.24, R.75, Q.151, E.153, F.174, G.176, P.177, S.178, L.216 Ligands: PO4.8, MG.9 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Q.151, C:S.178 Water bridges: C:R.75, C:R.75 Salt bridges: C:R.75 PO4.8: 6 residues within 4Å: Chain C: W.24, R.75, L.216 Chain E: S.124, V.125 Ligands: PO4.7 10 PLIP interactions: 6 interactions with chain C, 4 interactions with chain E Hydrogen bonds: C:W.24, C:R.75, E:V.125 Water bridges: C:S.238, C:S.238, C:S.238, C:S.238, E:S.124, E:S.126, E:S.126 PO4.10: 11 residues within 4Å: Chain D: W.24, R.75, Q.151, E.153, F.174, G.176, P.177, S.178, L.216 Ligands: PO4.11, MG.12 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:E.153, D:S.178 Water bridges: D:R.75, D:Q.151, D:E.153, B:V.123 Salt bridges: D:R.75 PO4.11: 6 residues within 4Å: Chain B: S.124, V.125 Chain D: W.24, R.75, L.216 Ligands: PO4.10 11 PLIP interactions: 6 interactions with chain B, 5 interactions with chain D Hydrogen bonds: B:S.124, B:S.124, B:V.125, D:R.75 Water bridges: B:S.124, B:S.126, B:S.126, D:D.47, D:S.238, D:S.238, D:S.238 PO4.13: 11 residues within 4Å: Chain E: W.24, R.75, Q.151, E.153, F.174, G.176, P.177, S.178, L.216 Ligands: PO4.14, MG.15 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:Q.151, E:S.178 Water bridges: E:R.75, E:R.75 Salt bridges: E:R.75 PO4.14: 6 residues within 4Å: Chain A: S.124, V.125 Chain E: W.24, R.75, L.216 Ligands: PO4.13 10 PLIP interactions: 4 interactions with chain A, 6 interactions with chain E Hydrogen bonds: A:V.125, E:W.24, E:R.75 Water bridges: A:S.124, A:S.126, A:S.126, E:S.238, E:S.238, E:S.238, E:S.238 PO4.16: 11 residues within 4Å: Chain F: W.24, R.75, Q.151, E.153, F.174, G.176, P.177, S.178, L.216 Ligands: PO4.17, MG.18 7 PLIP interactions: 6 interactions with chain F, 1 interactions with chain D Hydrogen bonds: F:E.153, F:S.178 Water bridges: F:R.75, F:Q.151, F:E.153, D:V.123 Salt bridges: F:R.75 PO4.17: 6 residues within 4Å: Chain D: S.124, V.125 Chain F: W.24, R.75, L.216 Ligands: PO4.16 11 PLIP interactions: 6 interactions with chain D, 5 interactions with chain F Hydrogen bonds: D:S.124, D:S.124, D:V.125, F:R.75 Water bridges: D:S.124, D:S.126, D:S.126, F:D.47, F:S.238, F:S.238, F:S.238

6 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: R.75, Q.151, E.153, D.179 Ligands: PO4.1 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.153, A:D.179, H2O.4, H2O.13, H2O.33 MG.6: 5 residues within 4Å: Chain B: R.75, Q.151, E.153, D.179 Ligands: PO4.4 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.153, B:D.179, H2O.16, H2O.26, H2O.71 MG.9: 5 residues within 4Å: Chain C: R.75, Q.151, E.153, D.179 Ligands: PO4.7 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.153, C:D.179, H2O.29, H2O.38, H2O.58 MG.12: 5 residues within 4Å: Chain D: R.75, Q.151, E.153, D.179 Ligands: PO4.10 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:E.153, D:D.179, H2O.20, H2O.42, H2O.51 MG.15: 5 residues within 4Å: Chain E: R.75, Q.151, E.153, D.179 Ligands: PO4.13 5 PLIP interactions: 2 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:E.153, E:D.179, H2O.8, H2O.54, H2O.63 MG.18: 5 residues within 4Å: Chain F: R.75, Q.151, E.153, D.179 Ligands: PO4.16 5 PLIP interactions: 2 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:E.153, F:D.179, H2O.46, H2O.67, H2O.76

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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