SMTL ID : 1p5b.1

High Resolution Structure of Reduced Active Mutant of (S)-Mandelate Dehydrogenase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 7 residues within 4Å: Chain A: Y.26, Y.131, R.165, H.255, R.258, Q.259 Ligands: FMN.2 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:Y.131, A:Q.259 Water bridges: A:G.81, A:Y.131, A:R.165, A:R.165, A:R.165 Salt bridges: A:R.165, A:H.255, A:R.258 SO4.4: 7 residues within 4Å: Chain B: Y.26, Y.131, R.165, H.255, R.258, Q.259 Ligands: FMN.5 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:Y.131, B:Q.259 Water bridges: B:G.81, B:Y.131, B:R.165, B:R.165, B:R.165 Salt bridges: B:R.165, B:H.255, B:R.258 SO4.7: 7 residues within 4Å: Chain C: Y.26, Y.131, R.165, H.255, R.258, Q.259 Ligands: FMN.8 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:Y.131, C:Q.259 Water bridges: C:G.81, C:Y.131, C:R.165, C:R.165, C:R.165 Salt bridges: C:R.165, C:H.255, C:R.258 SO4.10: 7 residues within 4Å: Chain D: Y.26, Y.131, R.165, H.255, R.258, Q.259 Ligands: FMN.11 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:Y.131, D:Q.259 Water bridges: D:G.81, D:Y.131, D:R.165, D:R.165, D:R.165 Salt bridges: D:R.165, D:H.255, D:R.258

4 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 21 residues within 4Å: Chain A: Y.26, L.27, P.79, T.80, G.81, S.108, Q.129, Y.131, T.156, K.231, S.253, H.255, G.256, R.258, D.284, S.285, G.286, R.288, G.307, R.308 Ligands: SO4.1 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:Y.26, A:T.80, A:R.308 Hydrogen bonds: A:P.79, A:G.81, A:S.108, A:Q.129, A:Q.129, A:Y.131, A:T.156, A:K.231, A:K.231, A:S.253, A:S.285, A:G.286, A:G.307, A:R.308 Water bridges: A:H.255, A:F.287, A:F.287, A:R.288, A:R.288 Salt bridges: A:R.288, A:R.308 FMN.5: 21 residues within 4Å: Chain B: Y.26, L.27, P.79, T.80, G.81, S.108, Q.129, Y.131, T.156, K.231, S.253, H.255, G.256, R.258, D.284, S.285, G.286, R.288, G.307, R.308 Ligands: SO4.4 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:Y.26, B:T.80, B:R.308 Hydrogen bonds: B:P.79, B:G.81, B:S.108, B:Q.129, B:Q.129, B:Y.131, B:T.156, B:K.231, B:K.231, B:S.253, B:S.285, B:G.286, B:G.307, B:R.308 Water bridges: B:H.255, B:F.287, B:F.287, B:R.288, B:R.288 Salt bridges: B:R.288, B:R.308 FMN.8: 21 residues within 4Å: Chain C: Y.26, L.27, P.79, T.80, G.81, S.108, Q.129, Y.131, T.156, K.231, S.253, H.255, G.256, R.258, D.284, S.285, G.286, R.288, G.307, R.308 Ligands: SO4.7 24 PLIP interactions: 24 interactions with chain C Hydrophobic interactions: C:Y.26, C:T.80, C:R.308 Hydrogen bonds: C:P.79, C:G.81, C:S.108, C:Q.129, C:Q.129, C:Y.131, C:T.156, C:K.231, C:K.231, C:S.253, C:S.285, C:G.286, C:G.307, C:R.308 Water bridges: C:H.255, C:F.287, C:F.287, C:R.288, C:R.288 Salt bridges: C:R.288, C:R.308 FMN.11: 21 residues within 4Å: Chain D: Y.26, L.27, P.79, T.80, G.81, S.108, Q.129, Y.131, T.156, K.231, S.253, H.255, G.256, R.258, D.284, S.285, G.286, R.288, G.307, R.308 Ligands: SO4.10 24 PLIP interactions: 24 interactions with chain D Hydrophobic interactions: D:Y.26, D:T.80, D:R.308 Hydrogen bonds: D:P.79, D:G.81, D:S.108, D:Q.129, D:Q.129, D:Y.131, D:T.156, D:K.231, D:K.231, D:S.253, D:S.285, D:G.286, D:G.307, D:R.308 Water bridges: D:H.255, D:F.287, D:F.287, D:R.288, D:R.288 Salt bridges: D:R.288, D:R.308

4 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.3: 3 residues within 4Å: Chain A: W.87, P.88, K.89 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.96 Salt bridges: A:K.89 MES.6: 3 residues within 4Å: Chain B: W.87, P.88, K.89 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.96 Salt bridges: B:K.89 MES.9: 3 residues within 4Å: Chain C: W.87, P.88, K.89 2 PLIP interactions: 2 interactions with chain C Water bridges: C:R.96 Salt bridges: C:K.89 MES.12: 3 residues within 4Å: Chain D: W.87, P.88, K.89 2 PLIP interactions: 2 interactions with chain D Water bridges: D:R.96 Salt bridges: D:K.89

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sukumar, N. et al., High resolution structures of an oxidized and reduced flavoprotein. The water switch in a soluble form of (S)-mandelate dehydrogenase. J.Biol.Chem. (2004)

Release Date

2003-10-28

Peptides

L(+)-Mandelate Dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

L(+)-Mandelate Dehydrogenase

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