SMTL ID : 5zi4.1

MDH3 wild type, nad-oaa-form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x OAA: OXALOACETATE ION(Non-covalent)

OAA.1: 7 residues within 4Å: Chain A: R.82, N.120, R.154, H.189, G.222, A.235 Ligands: NAD.2 6 PLIP interactions: 6 interactions with chain A Water bridges: A:R.82, A:R.154, A:A.235 Salt bridges: A:R.82, A:R.154, A:H.189 OAA.3: 7 residues within 4Å: Chain B: R.82, N.120, R.154, H.189, G.222, A.235 Ligands: NAD.4 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.120 Water bridges: B:A.235 Salt bridges: B:R.82, B:R.154, B:H.189

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

NAD.2: 26 residues within 4Å: Chain A: G.10, S.12, G.13, G.14, V.15, Y.35, D.36, I.37, P.77, A.78, G.79, V.80, P.81, N.95, I.98, L.102, I.118, S.119, N.120, V.122, V.147, H.189, A.235, T.236, M.239 Ligands: OAA.1 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:M.239 Hydrogen bonds: A:S.12, A:S.12, A:G.14, A:V.15, A:I.37, A:G.79, A:N.95, A:I.118, A:N.120 Water bridges: A:G.13, A:G.16, A:R.38 NAD.4: 27 residues within 4Å: Chain B: G.10, S.12, G.13, G.14, V.15, Y.35, D.36, I.37, P.77, A.78, G.79, V.80, P.81, N.95, I.98, L.102, I.118, S.119, N.120, V.122, V.147, L.150, H.189, A.235, T.236, M.239 Ligands: OAA.3 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:L.150, B:M.239 Hydrogen bonds: B:S.12, B:G.14, B:V.15, B:I.37, B:G.79, B:V.80, B:N.95, B:I.118, B:N.120 Water bridges: B:G.13, B:G.16, B:S.101, B:S.101, B:N.120, B:S.234, B:S.234

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Moriyama, S. et al., Structure of glyoxysomal malate dehydrogenase (MDH3) from Saccharomyces cerevisiae. Acta Crystallogr F Struct Biol Commun (2018)

Release Date

2018-10-24

Peptides

Malate dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Malate dehydrogenase

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