SMTL ID : 8oro.1

CRYSTAL STRUCTURE OF THE COFACTOR-DEVOID 1-H-3-HYDROXY-4- OXOQUINALDINE 2,4-DIOXYGENASE (HOD) S101A VARIANT COMPLEXED WITH 2-METHYL-QUINOLIN-4(1H)-ONE UNDER HYPEROXYC CONDITIONS

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x VFH: 2-methyl-quinolin-4(1H)-one(Non-covalent)

VFH.1: 12 residues within 4Å: Chain A: W.48, H.50, A.113, H.114, L.155, W.172, M.189, W.197, S.200, I.204, H.263 Ligands: OXY.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.48, A:L.155, A:W.172, A:W.197, A:I.204 Hydrogen bonds: A:W.48 VFH.5: 12 residues within 4Å: Chain B: W.48, H.50, A.113, H.114, L.155, W.172, M.189, W.197, S.200, I.204, H.263 Ligands: OXY.6 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:W.48, B:L.155, B:W.172, B:W.197, B:I.204 Hydrogen bonds: B:W.48, B:W.48

2 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.2: 5 residues within 4Å: Chain A: G.47, W.48, A.113, H.114 Ligands: VFH.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.48, A:H.114 Water bridges: A:G.47 OXY.6: 5 residues within 4Å: Chain B: G.47, W.48, A.113, H.114 Ligands: VFH.5 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.48, B:H.114 Water bridges: B:G.47

4 x TAR: D(-)-TARTARIC ACID(Non-covalent)

TAR.3: 2 residues within 4Å: Chain A: R.272, V.275 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.272 Salt bridges: A:R.272 TAR.4: 3 residues within 4Å: Chain A: K.257, L.258, G.259 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.257, A:L.258 TAR.7: 3 residues within 4Å: Chain B: K.179, R.182, H.183 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:K.179, B:K.179 Water bridges: B:E.187, B:E.187 Salt bridges: B:K.179, B:K.179, B:R.182, B:H.183 TAR.8: 2 residues within 4Å: Chain B: H.176, D.177 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.177 Water bridges: B:D.177 Salt bridges: B:H.176

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 5 residues within 4Å: Chain A: P.84 Chain B: E.121, E.124, M.217, L.221 1 PLIP interactions: 1 interactions with chain B Water bridges: B:N.211

1 x NA: SODIUM ION(Non-functional Binders)

NA.10: 4 residues within 4Å: Chain B: A.247, H.250, P.251, F.253 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.251

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bui, S. et al., Evolutionary adaptation from hydrolytic to oxygenolytic catalysis at the alpha / beta-hydrolase fold. Chem Sci (2023)

Release Date

2024-01-17

Peptides

1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
BBB

1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase

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