SMTL ID : 6itk.1

Crystal structure of malate dehydrogenase from Corynebacterium glutamicum ATCC 13032 in complex with NAD and malate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x LMR: (2S)-2-hydroxybutanedioic acid(Non-covalent)

LMR.1: 6 residues within 4Å: Chain A: N.136, R.167, H.192, G.231, S.242 Ligands: NAD.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.136, A:H.192 Water bridges: A:G.231, A:S.242 Salt bridges: A:R.167 LMR.3: 6 residues within 4Å: Chain B: N.136, R.167, H.192, G.231, S.242 Ligands: NAD.4 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.136, B:H.192 Water bridges: B:G.231, B:S.242 Salt bridges: B:R.167, B:H.192

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

NAD.2: 21 residues within 4Å: Chain A: G.16, A.18, G.19, Q.20, I.21, E.47, I.48, A.51, V.92, G.93, A.94, I.113, Q.117, V.134, G.135, N.136, M.160, L.163, H.192, A.246 Ligands: LMR.1 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:I.21, A:L.163, A:A.246 Hydrogen bonds: A:G.16, A:Q.20, A:Q.20, A:I.21, A:A.94, A:N.136, A:N.136, A:M.160 Water bridges: A:G.19, A:S.22, A:H.192, A:H.192 NAD.4: 24 residues within 4Å: Chain B: G.16, A.18, G.19, Q.20, I.21, L.46, E.47, I.48, A.51, V.92, G.93, A.94, P.96, I.113, Q.117, V.134, G.135, N.136, M.160, L.163, H.192, S.242, A.246 Ligands: LMR.3 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:I.21, B:L.163, B:A.246 Hydrogen bonds: B:G.16, B:Q.20, B:I.21, B:A.94, B:N.136, B:N.136, B:M.160 Water bridges: B:G.19, B:S.22

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ahn, J.H. et al., Enhanced succinic acid production by Mannheimia employing optimal malate dehydrogenase. Nat Commun (2020)

Release Date

2019-11-27

Peptides

Malate dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Malate dehydrogenase