SMTL ID : 4qgn.1

Human acireductone dioxygenase with iron ion and L-methionine in active center

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.05 Å

Oligo State

monomer

Ligands

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

FE.1: 5 residues within 4Å: Chain A: H.92, H.94, E.98, H.137 Ligands: MSE.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.92, A:H.94, A:E.98, A:H.137, MSE.4

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

CL.2: 3 residues within 4Å: Chain A: F.88, R.100, R.151 Ligand excluded by PLIP CL.3: 2 residues within 4Å: Chain A: N.80, Y.81 Ligand excluded by PLIP

1 x MSE: SELENOMETHIONINE(Non-functional Binders)

MSE.4: 11 residues within 4Å: Chain A: M.87, F.88, H.92, H.94, E.98, R.100, H.137, F.139, A.161 Ligands: FE.1, ACT.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.98, A:R.100 Salt bridges: A:H.92, A:H.137

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

SO4.5: 5 residues within 4Å: Chain A: W.9, R.23, G.27, R.28, P.29 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.23 SO4.6: 3 residues within 4Å: Chain A: R.60, S.66, M.68 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.66 Salt bridges: A:R.60 SO4.7: 2 residues within 4Å: Chain A: E.57, R.61 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.61 SO4.8: 4 residues within 4Å: Chain A: E.91, R.112, W.118, R.138 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.138 Salt bridges: A:R.112

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

ACT.9: 10 residues within 4Å: Chain A: H.94, D.97, E.98, I.99, R.100, L.152, F.153, V.158, W.159 Ligands: MSE.4 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.153, A:W.159 Water bridges: A:D.96 Salt bridges: A:H.94, A:R.100

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Milaczewska, A. et al., On the Structure and Reaction Mechanism of Human Acireductone Dioxygenase. Chemistry (2018)

Release Date

2015-05-27

Peptides

1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase