SMTL ID : 6itl.1

Crystal structure of malate dehydrogenase from Mannheimia succiniciproducens in complex with NAD

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

homo-dimer

Ligands

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

NAD.1: 27 residues within 4Å: Chain A: G.7, A.9, G.10, G.11, I.12, Y.33, D.34, V.35, S.76, A.77, G.78, V.79, A.80, L.90, N.94, I.97, L.101, I.117, T.118, N.119, V.121, I.146, L.149, H.177, A.224, T.225, M.228 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.149 Hydrogen bonds: A:G.11, A:I.12, A:V.35, A:G.78, A:V.79, A:N.94, A:I.117, A:N.119, A:N.119 Water bridges: A:G.10, A:G.13, A:A.80, A:S.223 NAD.3: 27 residues within 4Å: Chain B: G.7, A.9, G.10, G.11, I.12, Y.33, D.34, V.35, S.76, A.77, G.78, V.79, A.80, L.90, N.94, I.97, L.101, I.117, T.118, N.119, V.121, I.146, L.149, H.177, A.224, T.225, M.228 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:L.149 Hydrogen bonds: B:G.11, B:I.12, B:V.35, B:G.78, B:V.79, B:N.94, B:I.117, B:N.119, B:N.119 Water bridges: B:G.10, B:G.13, B:Y.33, B:Y.33, B:A.80, B:S.223

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 10 residues within 4Å: Chain A: M.1, D.71, I.72, C.113, L.239, S.243, G.271, T.272, E.273, G.274 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.71, A:G.274, A:G.274 GOL.4: 10 residues within 4Å: Chain B: M.1, D.71, I.72, C.113, L.239, S.243, G.271, T.272, E.273, G.274 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.71, B:G.274, B:G.274

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
A

Malate dehydrogenase