SMTL ID : 5zi2.1

MDH3 wild type, nad-form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: Y.35, I.64, S.101, L.102 Ligands: NAD.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.101

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

NAD.2: 25 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.147, H.189, A.235, T.236, M.239 Ligands: GOL.1 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:M.239 Hydrogen bonds: A:S.12, A:G.14, A:V.15, A:I.37, A:G.79, A:V.80, A:V.80, A:N.95, A:N.120, A:N.120, A:V.147 Water bridges: A:G.13, A:G.16, A:R.38, A:R.82

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 3 residues within 4Å: Chain A: A.110, P.111, N.112 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain B: A.110, P.111, N.112 Ligand excluded by PLIP

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.5: 13 residues within 4Å: Chain B: G.10, S.12, G.13, G.14, V.15, Y.35, D.36, I.37, A.78, G.79, P.81, I.98, L.102 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.12, B:G.14, B:V.15, B:I.37, B:G.79 Water bridges: B:G.13, B:G.16, B:S.101

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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