SMTL ID : 5v4p.3 (2 other biounits)

Saccharomyces cerevisiae OYE 3 soaked with p-hydroxybenzaldehyde

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

homo-dimer

Ligands

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 19 residues within 4Å: Chain A: P.35, P.36, L.37, T.38, G.73, Q.115, H.192, N.195, R.244, V.293, P.296, G.325, N.326, Y.347, G.348, R.349, F.375, Y.376 Ligands: HBA.2 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:L.37, A:R.349, A:F.375, A:Y.376 Hydrogen bonds: A:P.36, A:T.38, A:G.73, A:Q.115, A:Q.115, A:N.195, A:R.244, A:R.244, A:N.326, A:G.348, A:R.349 Water bridges: A:E.300, A:E.300, A:G.325, A:Y.327, A:Y.347, A:F.350 Salt bridges: A:R.349 FMN.6: 19 residues within 4Å: Chain B: P.35, P.36, L.37, T.38, G.73, Q.115, H.192, N.195, R.244, V.293, P.296, G.325, N.326, Y.347, G.348, R.349, F.375, Y.376 Ligands: HBA.7 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:L.37, B:R.349, B:F.375, B:F.375, B:Y.376 Hydrogen bonds: B:P.36, B:T.38, B:T.38, B:G.73, B:Q.115, B:Q.115, B:N.195, B:R.244, B:R.244, B:N.326, B:G.348, B:R.349 Water bridges: B:G.325, B:G.325, B:F.350 Salt bridges: B:R.349

2 x HBA: P-HYDROXYBENZALDEHYDE(Non-covalent)

HBA.2: 9 residues within 4Å: Chain A: T.38, W.117, H.192, N.195, Y.197, F.251, P.296, Y.376 Ligands: FMN.1 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.117, A:Y.197, A:F.251, A:P.296 Hydrogen bonds: A:N.195 HBA.7: 8 residues within 4Å: Chain B: T.38, W.117, H.192, N.195, Y.197, P.296, Y.376 Ligands: FMN.6 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:W.117, B:N.195, B:Y.197, B:P.296 Hydrogen bonds: B:N.195, B:Y.376

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

NA.3: 2 residues within 4Å: Chain A: N.180 Ligands: TOE.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.180, A:N.180 NA.8: 2 residues within 4Å: Chain B: N.180 Ligands: TOE.9 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.180, B:N.180

4 x TOE: 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL(Non-covalent)

TOE.4: 6 residues within 4Å: Chain A: W.90, S.91, D.92, H.176, N.180 Ligands: NA.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.92, A:N.180 TOE.5: 3 residues within 4Å: Chain A: D.92, A.96, K.99 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.99 TOE.9: 7 residues within 4Å: Chain B: W.90, D.92, H.176, K.179, N.180, A.183 Ligands: NA.8 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.180 TOE.10: 5 residues within 4Å: Chain B: D.92, V.95, A.96, K.99, A.183 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.99

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stewart, J. et al., Saccharomyces cerevisiae OYE 3 soaked with p-hydroxybenzaldehyde. To Be Published

Release Date

2018-03-14

Peptides

NADPH dehydrogenase 3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

NADPH dehydrogenase 3

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