SMTL ID : 5x20.3 (2 other biounits)

The ternary structure of D-mandelate dehydrogenase with NADH and anilino(oxo)acetate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

1 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 22 residues within 4Å: Chain A: G.9, A.10, M.11, D.30, W.32, H.35, F.77, T.78, K.79, Q.82, L.104, N.105, W.129, T.130, A.131, L.133, K.187, S.260, R.270, E.273 Ligands: AOT.2, GOL.5 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:A.8, A:A.10, A:M.11, A:T.78, A:Q.82, A:N.105, A:N.105, A:A.131, A:A.131, A:S.260, A:R.270, A:E.273 Water bridges: A:G.9, A:G.12, A:G.31, A:K.79, A:K.79 Salt bridges: A:K.79, A:K.79, A:R.270 pi-Stacking: A:W.32, A:W.32 pi-Cation interactions: A:R.270

1 x AOT: 2-oxidanylidene-2-phenylazanyl-ethanoic acid(Non-covalent)

AOT.2: 12 residues within 4Å: Chain A: N.105, M.128, T.130, K.187, V.190, N.191, N.195, C.248, I.254, P.259, S.260 Ligands: NAD.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:T.130, A:V.190, A:I.254 Hydrogen bonds: A:N.105, A:K.187, A:N.191, A:N.195, A:S.260 Water bridges: A:Y.258 Salt bridges: A:K.187

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: I.107, G.108, E.110, H.181, I.184, Y.185, E.232, I.234 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.108, A:E.232 GOL.4: 8 residues within 4Å: Chain A: R.14, T.130, A.131, G.132, K.140, L.141, F.142, H.257 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.14, A:T.130, A:F.142, A:H.257 Water bridges: A:T.130 GOL.5: 7 residues within 4Å: Chain A: W.32, L.133, E.134, G.135, N.268, R.270 Ligands: NAD.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.134, A:R.270 GOL.8: 5 residues within 4Å: Chain B: V.190, N.191, N.195, P.259, S.260 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.190, B:N.191, B:N.195, B:S.260

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

SO4.6: 4 residues within 4Å: Chain A: D.111, R.283, K.284, K.287 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.284 Salt bridges: A:K.284, A:K.287 SO4.7: 5 residues within 4Å: Chain A: N.151, D.154, G.155, K.156, E.157 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.151, A:G.155, A:K.156, A:E.157, A:E.157

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Furukawa, N. et al., The ternary complex structure of d-mandelate dehydrogenase with NADH and anilino(oxo)acetate. Biochem. Biophys. Res. Commun. (2017)

Release Date

2017-04-05

Peptides

2-dehydropantoate 2-reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

2-dehydropantoate 2-reductase

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