SMTL ID : 5d2g.1

4-oxalocrotonate decarboxylase from Pseudomonas putida G7 - complexed with magnesium

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: K.83, M.84, E.128, E.130, E.161 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.128, A:E.130, A:E.161, H2O.3, H2O.4, H2O.4

8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 6 residues within 4Å: Chain A: G.85, L.86, I.101, E.128, I.163, A.182 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.86, A:E.128 Water bridges: A:K.83 EDO.3: 6 residues within 4Å: Chain A: Y.62, Y.102, L.237, E.240, R.241 Ligands: EDO.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.102, A:Y.102 EDO.4: 6 residues within 4Å: Chain A: Y.167, N.169, K.171, F.172, D.173, V.177 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.169, A:D.173, A:D.173 Water bridges: A:S.165, A:S.165, A:S.165 EDO.5: 6 residues within 4Å: Chain A: F.58, V.97, E.98, T.99, L.237 Ligands: EDO.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.98, A:T.99, A:T.99 EDO.6: 5 residues within 4Å: Chain A: R.69, I.79, G.81, L.82, T.249 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.69 Water bridges: A:V.80 EDO.7: 3 residues within 4Å: Chain A: G.76, N.77, D.107 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.77 Water bridges: A:D.107 EDO.8: 4 residues within 4Å: Chain A: L.30, E.67, R.70, R.71 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.70 Water bridges: A:R.26 EDO.9: 3 residues within 4Å: Chain A: N.211, G.212, N.267 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.267 Water bridges: A:G.212, A:N.267, A:N.267

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

CL.10: 2 residues within 4Å: Chain A: D.118, R.186 Ligand excluded by PLIP CL.11: 1 residues within 4Å: Chain A: R.70 Ligand excluded by PLIP

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.12: 3 residues within 4Å: Chain A: N.169, F.170, K.171 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.169, A:F.170, A:K.171 Water bridges: A:K.48, A:K.48, A:K.48 Salt bridges: A:K.171

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.13: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.151

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guimaraes, S.L. et al., Crystal Structures of Apo and Liganded 4-Oxalocrotonate Decarboxylase Uncover a Structural Basis for the Metal-Assisted Decarboxylation of a Vinylogous beta-Keto Acid. Biochemistry (2016)

Release Date

2016-05-04

Peptides

4-oxalocrotonate decarboxylase NahK: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

4-oxalocrotonate decarboxylase NahK

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