SMTL ID : 5yw0.1

Crystal structure of the Kdo hydroxylase KdoO, a non-heme Fe(II) alphaketoglutarate dependent dioxygenase in complex with succinate and Fe(III)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.49 Å

Oligo State

monomer

Ligands

5 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.1: 5 residues within 4Å: Chain A: I.178, G.179, P.239, Q.240, V.241 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.179 PG4.2: 2 residues within 4Å: Chain A: F.202, Y.205 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.205 PG4.3: 6 residues within 4Å: Chain A: R.76, A.122, R.123, R.162, T.272, H.274 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.76, A:R.76, A:R.123, A:R.162, A:T.272 PG4.4: 3 residues within 4Å: Chain A: Y.205, G.212, Y.213 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.213 PG4.5: 2 residues within 4Å: Chain A: Q.192, L.230 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.230 Water bridges: A:L.232

1 x FE: FE (III) ION(Non-covalent)

FE.6: 5 residues within 4Å: Chain A: H.146, D.148, H.260 Ligands: SIN.8, ACT.9 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.146, A:D.148, A:H.260, H2O.1, H2O.1

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 9 residues within 4Å: Chain A: P.12, G.40, I.178, G.179, E.180, P.181, Q.257, V.258, L.259 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.259 Water bridges: A:S.39, A:G.40, A:F.182, A:F.182

1 x SIN: SUCCINIC ACID(Non-covalent)

SIN.8: 11 residues within 4Å: Chain A: R.127, D.142, H.146, R.162, R.174, W.176, H.260, V.262, L.268 Ligands: FE.6, ACT.9 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.176, A:V.262 Hydrogen bonds: A:R.162 Water bridges: A:R.127, A:R.134 Salt bridges: A:R.127, A:R.127, A:H.146, A:R.174, A:H.260

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

ACT.9: 5 residues within 4Å: Chain A: D.142, F.150, R.162 Ligands: FE.6, SIN.8 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.162 Salt bridges: A:R.127, A:R.162 ACT.10: 5 residues within 4Å: Chain A: G.156, G.157, L.288, V.300, E.303 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.300, A:E.303 Hydrogen bonds: A:G.156 Water bridges: A:V.277 ACT.11: 3 residues within 4Å: Chain A: K.200, L.204, R.214 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.204 Salt bridges: A:K.200, A:R.214 ACT.12: 3 residues within 4Å: Chain A: K.276, N.278, S.304 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.278, A:S.304 Water bridges: A:N.278 Salt bridges: A:K.276

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joo, S.H. et al., Biochemical and Structural Insights into an Fe(II)/ alpha-Ketoglutarate/O2-Dependent Dioxygenase, Kdo 3-Hydroxylase (KdoO). J. Mol. Biol. (2018)

Release Date

2018-09-05

Peptides

Uncharacterized protein KdoO: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Uncharacterized protein KdoO

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