SMTL ID : 8jdx.1

Crystal structure of mLDHD in complex with 2-ketoisovaleric acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.79 Å

Oligo State

monomer

Ligands

1 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.1: 36 residues within 4Å: Chain A: E.45, P.81, F.82, G.83, T.84, G.85, T.86, G.87, G.91, V.92, L.103, P.145, G.146, A.147, A.149, S.150, C.152, G.153, M.154, A.156, T.157, A.159, S.160, E.213, G.214, G.217, I.218, I.219, W.338, Y.339, H.385, E.429, H.430, N.466 Ligands: MN.2, KIV.3 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:E.45, A:A.147, A:W.338, A:Y.339 Hydrogen bonds: A:G.83, A:T.84, A:T.84, A:T.84, A:G.85, A:T.86, A:T.86, A:T.86, A:G.87, A:G.91, A:G.146, A:S.150, A:T.157, A:S.160, A:I.219, A:I.219, A:E.429, A:N.466 Water bridges: A:T.157, A:E.213, A:E.213, A:H.430 pi-Stacking: A:H.430

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 5 residues within 4Å: Chain A: H.385, H.392, E.429 Ligands: FAD.1, KIV.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.385, A:H.392, A:E.429

1 x KIV: 3-METHYL-2-OXOBUTANOIC ACID(Non-covalent)

KIV.3: 9 residues within 4Å: Chain A: R.334, W.338, H.385, H.392, I.394, E.429, H.430 Ligands: FAD.1, MN.2 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.338, A:I.394 Water bridges: A:G.146, A:R.334 Salt bridges: A:R.334, A:H.385, A:H.392

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jin, S. et al., Lactate dehydrogenase D is a general dehydrogenase for D-2-hydroxyacids and is associated with D-lactic acidosis. Nat Commun (2023)

Release Date

2023-10-18

Peptides

Probable D-lactate dehydrogenase, mitochondrial: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Probable D-lactate dehydrogenase, mitochondrial

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