SMTL ID : 3b8i.2 (1 other biounit)

Crystal Structure of Oxaloacetate Decarboxylase from Pseudomonas Aeruginosa (PA4872) in complex with oxalate and Mg2+.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: D.61, D.88 Ligands: OXL.2 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.88, H2O.1, H2O.1, H2O.1 MG.5: 3 residues within 4Å: Chain B: D.88, D.90 Ligands: OXL.6 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.88, H2O.15, H2O.16, H2O.16 MG.8: 3 residues within 4Å: Chain C: D.61, D.88 Ligands: OXL.9 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.88, H2O.25, H2O.25, H2O.25 MG.12: 3 residues within 4Å: Chain D: D.88, D.90 Ligands: OXL.13 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.88, H2O.40, H2O.40, H2O.40

4 x OXL: OXALATE ION(Non-covalent)

OXL.2: 9 residues within 4Å: Chain A: G.48, G.49, S.50, D.61, D.88, R.159, Y.212, H.235 Ligands: MG.1 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.49, A:S.50, A:D.88 Water bridges: A:S.50, A:R.159, A:R.159, A:R.159, A:Y.212 Salt bridges: A:R.159, A:H.235, A:H.235 OXL.6: 8 residues within 4Å: Chain B: G.48, G.49, S.50, D.61, D.88, R.159, H.235 Ligands: MG.5 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:G.49, B:S.50, B:H.235 Water bridges: B:D.61, B:D.61, B:D.61, B:D.61, B:D.88, B:D.90 Salt bridges: B:R.159, B:H.235 OXL.9: 9 residues within 4Å: Chain C: G.48, G.49, S.50, D.61, D.88, R.159, Y.212, H.235 Ligands: MG.8 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:G.49, C:S.50, C:D.88, C:D.88, C:Y.212 Water bridges: C:S.50, C:S.50, C:R.159, C:R.159, C:R.159 Salt bridges: C:R.159, C:H.235, C:H.235 OXL.13: 8 residues within 4Å: Chain D: G.48, G.49, S.50, D.61, D.88, R.159, H.235 Ligands: MG.12 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:G.49, D:S.50, D:H.235 Water bridges: D:D.61, D:D.61, D:D.61, D:D.61, D:D.88, D:D.90 Salt bridges: D:R.159, D:H.235

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: E.107, R.108, V.150 Chain D: S.5, H.6 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain D Hydrogen bonds: A:E.107, A:E.107, D:H.6 Water bridges: A:R.10, A:R.10, A:R.108, D:S.5, D:H.7 GOL.4: 4 residues within 4Å: Chain A: T.130, D.131, L.132, L.164 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.164 GOL.7: 5 residues within 4Å: Chain B: E.107, R.108, V.150 Chain C: S.5, H.6 10 PLIP interactions: 3 interactions with chain C, 7 interactions with chain B Hydrogen bonds: C:H.6, B:E.107, B:E.107 Water bridges: C:S.5, C:H.7, B:R.10, B:R.10, B:R.10, B:V.104, B:R.108 GOL.10: 5 residues within 4Å: Chain B: S.5, H.6 Chain C: E.107, R.108, V.150 9 PLIP interactions: 6 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:E.107, C:E.107, C:E.107, B:H.6 Water bridges: C:R.10, C:R.10, C:R.108, B:S.5, B:H.7 GOL.11: 4 residues within 4Å: Chain C: T.130, D.131, L.132, L.164 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.131, C:L.164 GOL.14: 5 residues within 4Å: Chain A: S.5, H.6 Chain D: E.107, R.108, V.150 10 PLIP interactions: 4 interactions with chain A, 6 interactions with chain D Hydrogen bonds: A:H.6, D:E.107 Water bridges: A:S.5, A:H.6, A:H.7, D:R.10, D:R.10, D:R.10, D:V.104, D:R.108

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Narayanan, B.C. et al., Structure and function of PA4872 from Pseudomonas aeruginosa, a novel class of oxaloacetate decarboxylase from the PEP mutase/isocitrate lyase superfamily. Biochemistry (2008)

Release Date

2008-01-01

Peptides

PA4872 oxaloacetate decarboxylase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
E

D
F

PA4872 oxaloacetate decarboxylase

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