SMTL ID : 3c1t.2 (1 other biounit)

Binding of two substrate analogue molecules to dihydroflavonol 4-reductase alters the functional geometry of the catalytic site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-dimer

Ligands

2 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 26 residues within 4Å: Chain A: G.12, S.14, G.15, F.16, I.17, R.37, K.44, D.64, L.65, V.84, A.85, T.86, P.87, M.88, T.126, S.127, S.128, K.167, P.190, T.191, L.192, V.193, P.204, S.205 Ligands: MYC.2, MYC.3 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:I.17, A:P.190, A:V.193 Hydrogen bonds: A:G.12, A:S.14, A:S.14, A:F.16, A:I.17, A:R.37, A:R.37, A:D.64, A:L.65, A:V.84, A:T.86, A:M.88, A:K.167, A:V.193, A:S.205, A:S.205 Water bridges: A:G.15, A:G.18, A:R.37, A:R.37, A:R.37, A:D.38, A:S.205 Salt bridges: A:R.37, A:K.44 pi-Cation interactions: A:R.37 NAP.4: 27 residues within 4Å: Chain B: G.12, S.14, G.15, F.16, I.17, R.37, K.44, A.63, D.64, L.65, V.84, A.85, T.86, P.87, M.88, T.126, S.127, S.128, K.167, P.190, T.191, L.192, V.193, P.204, S.205 Ligands: MYC.5, MYC.6 27 PLIP interactions: 27 interactions with chain B Hydrophobic interactions: B:P.190, B:V.193 Hydrogen bonds: B:S.14, B:S.14, B:F.16, B:I.17, B:R.37, B:D.64, B:L.65, B:V.84, B:T.86, B:K.167, B:V.193, B:S.205, B:S.205 Water bridges: B:S.14, B:G.15, B:G.18, B:R.37, B:R.37, B:D.38, B:K.44, B:K.44, B:S.205 Salt bridges: B:R.37, B:K.44 pi-Cation interactions: B:R.37

4 x MYC: 3,5,7-TRIHYDROXY-2-(3,4,5-TRIHYDROXYPHENYL)-4H-CHROMEN-4-ONE(Non-covalent)

MYC.2: 15 residues within 4Å: Chain A: S.128, A.129, G.130, N.133, I.134, T.191, L.192, P.204, S.205, T.208, I.222, Q.227, F.292 Ligands: NAP.1, MYC.3 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:A.129, A:L.192, A:I.222, A:I.222 Hydrogen bonds: A:S.128, A:A.129, A:G.130, A:N.133, A:N.133, A:L.192, A:P.204, A:T.208, A:Q.227, A:Q.227, A:Q.227, A:Q.227 MYC.3: 14 residues within 4Å: Chain A: T.86, M.88, S.128, G.130, T.159, A.160, Y.163, F.164, K.167, H.219, S.221, I.222 Ligands: NAP.1, MYC.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:T.159, A:A.160, A:Y.163, A:F.164, A:I.222 Hydrogen bonds: A:S.128, A:S.128, A:G.130, A:A.218, A:H.219 Water bridges: A:S.221 MYC.5: 17 residues within 4Å: Chain B: M.88, S.128, A.129, G.130, N.133, I.134, P.190, T.191, L.192, P.204, S.205, T.208, I.222, Q.227, F.292 Ligands: NAP.4, MYC.6 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:A.129, B:L.192, B:I.222 Hydrogen bonds: B:S.128, B:A.129, B:G.130, B:N.133, B:N.133, B:L.192, B:P.204, B:T.208, B:Q.227, B:Q.227, B:Q.227 Water bridges: B:Q.227 MYC.6: 14 residues within 4Å: Chain B: T.86, M.88, S.128, G.130, T.159, A.160, Y.163, F.164, K.167, H.219, S.221, I.222 Ligands: NAP.4, MYC.5 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:T.159, B:A.160, B:Y.163, B:F.164, B:I.222 Hydrogen bonds: B:S.128, B:S.128, B:G.130, B:A.218, B:H.219 Water bridges: B:T.208, B:T.208, B:S.221

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Trabelsi, N. et al., Structural evidence for the inhibition of grape dihydroflavonol 4-reductase by flavonols. Acta Crystallogr.,Sect.D (2008)

Release Date

2008-02-19

Peptides

dihydroflavonol 4-reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

dihydroflavonol 4-reductase

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