SMTL ID : 6hl8.2 (1 other biounit)

Crystal Structure of the CsiD Glutarate Hydroxylase in complex with Glutarate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 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: GUA.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.180, A:D.182, A:H.312, H2O.6 FE2.3: 4 residues within 4Å: Chain B: H.180, D.182, H.312 Ligands: GUA.4 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.180, B:D.182, B:H.312, H2O.13 FE2.5: 4 residues within 4Å: Chain C: H.180, D.182, H.312 Ligands: GUA.6 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.180, C:D.182, C:H.312, H2O.19 FE2.7: 4 residues within 4Å: Chain D: H.180, D.182, H.312 Ligands: GUA.8 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.180, D:D.182, D:H.312, H2O.25

4 x GUA: GLUTARIC ACID(Non-covalent)

GUA.2: 9 residues within 4Å: Chain A: M.177, H.180, D.182, G.183, Y.185, F.267, R.329, R.331 Ligands: FE2.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.185, A:F.267 Hydrogen bonds: A:G.183, A:Y.185, A:R.329 Salt bridges: A:H.180, A:R.331 GUA.4: 9 residues within 4Å: Chain B: M.177, H.180, D.182, G.183, Y.185, F.267, R.329, R.331 Ligands: FE2.3 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.185, B:F.267 Hydrogen bonds: B:G.183, B:Y.185, B:R.329 Salt bridges: B:H.180, B:R.331 GUA.6: 9 residues within 4Å: Chain C: M.177, H.180, D.182, G.183, Y.185, F.267, R.329, R.331 Ligands: FE2.5 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:Y.185, C:F.267 Hydrogen bonds: C:G.183, C:Y.185, C:R.329 Salt bridges: C:H.180, C:R.331 GUA.8: 9 residues within 4Å: Chain D: M.177, H.180, D.182, G.183, Y.185, F.267, R.329, R.331 Ligands: FE2.7 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:Y.185, D:F.267 Hydrogen bonds: D:G.183, D:Y.185, D:R.329 Salt bridges: D:H.180, 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

2018-12-12

Peptides

Protein CsiD: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

C
B

D
B

Protein CsiD

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