SMTL ID : 6gpn.2 (1 other biounit)

Crystal Structure of the CsiD Glutarate Hydroxylase in complex with N-Oxalylglycine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

4 x FE2: FE (II) ION(Non-covalent)

FE2.1: 4 residues within 4Å: Chain A: H.180, D.182, H.312 Ligands: OGA.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.180, A:D.182, A:H.312 FE2.3: 4 residues within 4Å: Chain B: H.180, D.182, H.312 Ligands: OGA.4 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.180, B:D.182, B:H.312 FE2.5: 4 residues within 4Å: Chain C: H.180, D.182, H.312 Ligands: OGA.6 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.180, C:D.182, C:H.312 FE2.7: 4 residues within 4Å: Chain D: H.180, D.182, H.312 Ligands: OGA.8 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.180, D:D.182, D:H.312

4 x OGA: N-OXALYLGLYCINE(Non-covalent)

OGA.2: 11 residues within 4Å: Chain A: F.158, M.177, H.180, D.182, M.195, H.312, R.314, L.327, R.329, R.331 Ligands: FE2.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.182, A:R.325 Salt bridges: A:R.314, A:R.329, A:R.331 OGA.4: 11 residues within 4Å: Chain B: F.158, M.177, H.180, D.182, M.195, H.312, R.314, L.327, R.329, R.331 Ligands: FE2.3 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.182, B:R.325 Salt bridges: B:R.314, B:R.329, B:R.331 OGA.6: 11 residues within 4Å: Chain C: F.158, M.177, H.180, D.182, M.195, H.312, R.314, L.327, R.329, R.331 Ligands: FE2.5 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:D.182, C:R.325 Salt bridges: C:R.314, C:R.329, C:R.331 OGA.8: 11 residues within 4Å: Chain D: F.158, M.177, H.180, D.182, M.195, H.312, R.314, L.327, R.329, R.331 Ligands: FE2.7 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:D.182, D:R.325 Salt bridges: D:R.314, D:R.329, D:R.331

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Knorr, S. et al., Widespread bacterial lysine degradation proceeding via glutarate and L-2-hydroxyglutarate. Nat Commun (2018)

Release Date

2019-01-30

Peptides

Glutarate 2-hydroxylase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

C
B

D
B

Glutarate 2-hydroxylase

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