SMTL ID : 8qne.1

OPR3 variant with redesigned loop 6 (9aa)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 20 residues within 4Å: Chain A: A.39, P.40, M.41, T.42, G.73, Q.115, H.194, H.197, R.246, T.289, S.320, G.321, G.322, Y.342, G.343, R.344, F.370, Y.371 Ligands: MPD.2, MPD.4 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:M.41, A:R.344, A:F.370 Hydrogen bonds: A:P.40, A:T.42, A:T.42, A:G.73, A:Q.115, A:Q.115, A:R.246, A:R.246, A:S.320, A:G.321, A:G.322, A:G.343, A:R.344 Water bridges: A:T.289, A:Y.323, A:Y.323, A:R.344, A:L.345 Salt bridges: A:R.344

3 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.2: 7 residues within 4Å: Chain A: T.42, F.83, Y.199, H.253, Y.371 Ligands: FMN.1, MPD.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.199, A:Y.199 MPD.3: 5 residues within 4Å: Chain A: A.163, I.164, R.212, T.213, D.214 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.163, A:R.212, A:D.214 Hydrogen bonds: A:T.213, A:T.213 MPD.4: 6 residues within 4Å: Chain A: R.292, G.321, G.322, R.344 Ligands: FMN.1, MPD.2 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:R.292

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

SO4.5: 4 residues within 4Å: Chain A: Y.365, N.366, R.367, K.368 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.366, A:R.367, A:K.368 Water bridges: A:K.364, A:K.364 Salt bridges: A:K.364, A:R.367

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.6: 2 residues within 4Å: Chain A: F.384, L.385 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kerschbaumer, B. et al., Crystal structures of OPR3 wildtype and variants in complex with NAD(P)H. To Be Published

Release Date

2025-04-09

Peptides

12-oxophytodienoate reductase 3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

12-oxophytodienoate reductase 3

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