SMTL ID : 8qnk.1 (2 other biounits)

OPR3 variant R283D in complex with NADPH4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.91 Å

Oligo State

homo-dimer

Ligands

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 22 residues within 4Å: Chain A: A.36, P.37, M.38, T.39, G.70, Q.112, H.191, H.194, R.243, T.286, S.325, G.326, G.327, Y.328, Y.347, G.348, R.349, F.375, Y.376 Chain B: G.294, Q.295, E.297 21 PLIP interactions: 20 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:R.349, A:F.375, A:Y.376 Hydrogen bonds: A:P.37, A:T.39, A:T.39, A:G.70, A:Q.112, A:Q.112, A:R.243, A:R.243, A:S.325, A:G.326, A:G.327, A:Y.328, A:G.348, A:R.349, B:E.297 Water bridges: A:S.346, A:L.350 Salt bridges: A:R.349 FMN.4: 20 residues within 4Å: Chain A: Y.293 Chain B: A.36, P.37, M.38, T.39, G.70, Q.112, H.191, H.194, R.243, T.286, S.325, G.326, G.327, Y.347, G.348, R.349, F.375, Y.376 Ligands: MPD.3 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:M.38, B:R.349, B:F.375, B:F.375, B:Y.376 Hydrogen bonds: B:P.37, B:T.39, B:T.39, B:G.70, B:Q.112, B:Q.112, B:R.243, B:R.243, B:S.325, B:G.327, B:Y.328, B:G.348, B:R.349 Water bridges: B:G.326, B:G.326, B:G.326, B:L.350 Salt bridges: B:R.349

1 x 5J8: [[(2R,3S,4R,5R)-5-(5-aminocarbonyl-3,4-dihydro-2H-pyridin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-3-oxidanyl-4-phosphonooxy-oxolan-2-yl]methyl hydrogen phosphate(Non-covalent)

5J8.2: 10 residues within 4Å: Chain A: R.349, L.350, L.367, N.368, K.369, Y.370, R.372 Chain B: Y.290, G.294, R.300 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.350, A:K.369 Hydrogen bonds: A:L.367, A:Y.370, A:Y.370 Salt bridges: A:R.349, A:R.372, B:R.300 pi-Cation interactions: B:R.300, B:R.300

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

MPD.3: 9 residues within 4Å: Chain A: Y.293, G.294, Q.295 Chain B: F.80, H.194, Y.196, H.250, Y.376 Ligands: FMN.4 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:Q.295, B:Y.196 Hydrogen bonds: B:Y.376, B:Y.376

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

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

Release Date

2025-04-09

Peptides

12-oxophytodienoate reductase 3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

12-oxophytodienoate reductase 3

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