SMTL ID : 2w2l.2 (1 other biounit)

Crystal structure of the holo forms of Rhodotorula graminis D- mandelate dehydrogenase at 2.5A.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

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

NAD.1: 22 residues within 4Å: Chain A: T.117, G.170, G.172, A.173, I.174, Y.193, D.194, V.195, S.227, V.228, P.229, Y.230, M.231, T.234, T.255, A.256, R.257, D.281, H.304, G.306, G.307 Ligands: SO4.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:I.174 Hydrogen bonds: A:A.173, A:I.174, A:V.195, A:V.228, A:Y.230, A:D.281, A:D.281, A:G.306, A:G.307 Water bridges: A:G.111, A:G.172, A:Q.175 NAD.3: 20 residues within 4Å: Chain B: T.117, G.170, G.172, A.173, I.174, Y.193, D.194, V.195, V.228, P.229, Y.230, T.234, T.255, A.256, R.257, D.281, H.304, G.306, G.307 Ligands: SO4.4 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:T.117, B:I.174 Hydrogen bonds: B:A.173, B:I.174, B:V.195, B:V.228, B:Y.230, B:T.255, B:R.257, B:H.304, B:G.307 Water bridges: B:G.172, B:G.172, B:G.172, B:Q.175 pi-Cation interactions: B:R.257

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

SO4.2: 5 residues within 4Å: Chain A: G.88, A.89, G.90, R.257 Ligands: NAD.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.89, A:G.90 Salt bridges: A:R.257 SO4.4: 5 residues within 4Å: Chain B: G.88, A.89, G.90, R.257 Ligands: NAD.3 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.89, B:G.90 Water bridges: B:H.304 Salt bridges: B:R.257

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vachieri, S.G. et al., Crystal Structure of the Apo and Holo Forms of Rhodotorula Graminis D(-)-Mandelate Dehydrogenase. To be Published

Release Date

2009-11-17

Peptides

D-MANDELATE DEHYDROGENASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

D-MANDELATE DEHYDROGENASE

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