SMTL ID : 6w1k.4 (3 other biounits)

Crystal structure of the hydroxyglutarate synthase in complex with 2-oxoadipate from Oryza sativa

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

1 x NI: NICKEL (II) ION(Non-covalent)

NI.1: 6 residues within 4Å: Chain A: H.59, H.195, T.197, E.267, I.302 Ligands: OOG.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.59, A:H.195, A:E.267

1 x OOG: 2-OXOADIPIC ACID(Non-covalent)

OOG.2: 16 residues within 4Å: Chain A: H.59, A.61, R.63, F.123, S.125, N.194, H.195, Q.241, Y.265, E.267, F.294, E.295, A.299, I.302, F.303 Ligands: NI.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.123, A:A.299, A:F.303, A:F.303 Hydrogen bonds: A:Q.241, A:Y.265, A:I.302 Water bridges: A:A.299, A:A.299 Salt bridges: A:H.59, A:R.63, A:H.195

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

SO4.3: 1 residues within 4Å: Chain A: R.145 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.145, A:R.145, A:R.145, A:R.145 Salt bridges: A:R.145 SO4.4: 2 residues within 4Å: Chain A: V.175, R.178 No protein-ligand interaction detected (PLIP) SO4.5: 2 residues within 4Å: Chain A: G.229, I.230 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.230 Water bridges: A:G.229, A:L.231 SO4.6: 2 residues within 4Å: Chain A: D.206, R.208 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.206 Water bridges: A:K.212 Salt bridges: A:R.208

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thompson, M.G. et al., An iron (II) dependent oxygenase performs the last missing step of plant lysine catabolism. Nat Commun (2020)

Release Date

2020-06-24

Peptides

Hydroxyglutarate synthase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

Hydroxyglutarate synthase

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