SMTL ID : 5y9x.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.39 Å

Oligo State

monomer

Ligands

1 x CO: COBALT (II) ION(Non-covalent)

CO.1: 4 residues within 4Å: Chain A: H.146, D.148, H.260 Ligands: AKG.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.146, A:D.148, A:H.260, H2O.6

1 x AKG: 2-OXOGLUTARIC ACID(Non-covalent)

AKG.2: 12 residues within 4Å: Chain A: R.127, D.142, H.146, D.148, R.162, F.164, R.174, W.176, H.260, V.262, L.268 Ligands: CO.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.176, A:V.262 Hydrogen bonds: A:W.176 Water bridges: A:R.127, A:R.162, A:R.162 Salt bridges: A:R.127, A:R.127, A:R.162, A:R.174, A:H.260

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

PG4.3: 4 residues within 4Å: Chain A: E.22, R.99, E.102, K.103 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.103 Water bridges: A:R.99 PG4.4: 2 residues within 4Å: Chain A: A.106, H.109 No protein-ligand interaction detected (PLIP) PG4.5: 9 residues within 4Å: Chain A: R.201, Y.213, S.215, L.216, L.299, V.300, S.301, S.302 Ligands: ACT.14 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.201, A:R.201, A:L.216, A:S.301, A:S.302 PG4.6: 5 residues within 4Å: Chain A: R.177, Q.235, K.236, Q.240, D.263 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.240, A:D.263

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

SO4.7: 4 residues within 4Å: Chain A: S.117, S.118, K.120, K.276 4 PLIP interactions: 4 interactions with chain A Water bridges: A:S.118, A:K.276 Salt bridges: A:K.120, A:K.276 SO4.8: 5 residues within 4Å: Chain A: L.193, S.194, P.195, Y.220, L.295 1 PLIP interactions: 1 interactions with chain A Water bridges: A:L.193 SO4.9: 4 residues within 4Å: Chain A: R.76, A.122, H.274 Ligands: ACT.11 4 PLIP interactions: 4 interactions with chain A Water bridges: A:E.158, A:E.158 Salt bridges: A:R.76, A:H.274

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

ACT.10: 4 residues within 4Å: Chain A: K.140, F.150, P.151, S.152 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.152 Salt bridges: A:K.140 ACT.11: 7 residues within 4Å: Chain A: F.150, S.153, T.155, I.160, T.272, H.274 Ligands: SO4.9 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.150 Hydrogen bonds: A:S.153 Water bridges: A:E.158 Salt bridges: A:H.274 ACT.12: 3 residues within 4Å: Chain A: K.276, N.278, S.304 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:K.276 Hydrogen bonds: A:N.278, A:S.304, A:S.304 Water bridges: A:N.278 Salt bridges: A:K.276 ACT.13: 3 residues within 4Å: Chain A: E.292, N.296, K.297 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.292, A:N.296 ACT.14: 5 residues within 4Å: Chain A: P.198, G.199, R.201 Ligands: PG4.5, CL.18 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.199 Water bridges: A:K.200 Salt bridges: A:R.201 ACT.15: 2 residues within 4Å: Chain A: K.200, R.214 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.200, A:R.214

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.16: 7 residues within 4Å: Chain A: I.131, R.134, T.136, K.140, D.141, D.142, V.262 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.134, A:T.136, A:D.142 Water bridges: A:R.134, A:K.140, A:D.141, A:D.142

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

CL.17: 4 residues within 4Å: Chain A: F.16, D.17, I.29, K.32 Ligand excluded by PLIP CL.18: 5 residues within 4Å: Chain A: G.199, R.201, F.202, Y.213 Ligands: ACT.14 Ligand excluded by PLIP CL.19: 2 residues within 4Å: Chain A: K.86, S.87 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chung, H.S. et al., Biochemical and structural insights of Fe(II)/alpha-ketoglutarate/O2-dependent dioxygenase, KdoO from Methylacidiphilum infernorum V4. To Be Published

Release Date

2018-10-31

Peptides

Uncharacterized protein KdoO: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Uncharacterized protein KdoO

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