SMTL ID : 7by9.1

Malate Dehydrogenase from Geobacillus stearothermophilus (gs-MDH) complexed with Oxaloacetic Acid (OAA) and Nicotinamide Adenine Dinucleotide (NAD)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 24 residues within 4Å: Chain A: G.32, G.34, F.35, T.36, D.56, I.57, L.60, T.102, A.103, G.104, I.105, N.120, I.123, Q.126, V.127, L.143, T.144, N.145, V.147, Q.168, H.200, S.249, A.250 Ligands: OAA.2 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.143 Hydrogen bonds: A:G.32, A:F.35, A:T.36, A:T.36, A:G.104, A:I.105, A:N.120, A:N.145, A:N.145, A:N.145, A:Q.168 Water bridges: A:G.34, A:G.37 NAD.3: 22 residues within 4Å: Chain B: G.32, A.33, G.34, F.35, T.36, D.56, I.57, L.60, T.102, A.103, G.104, I.123, V.127, L.143, T.144, N.145, Q.168, L.172, H.200, A.250, P.254 Ligands: OAA.4 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:A.33, B:G.34, B:F.35, B:T.36, B:I.57, B:G.104, B:N.120, B:N.145, B:Q.168, B:Q.168 NAD.5: 21 residues within 4Å: Chain C: A.33, G.34, F.35, T.36, D.56, I.57, L.60, T.102, A.103, G.104, N.120, I.123, L.143, T.144, N.145, V.147, Q.168, H.200, A.250, P.254 Ligands: OAA.6 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:L.143, C:L.143, C:L.143, C:P.254 Hydrogen bonds: C:A.33, C:F.35, C:T.36, C:T.36, C:G.104, C:I.105, C:N.120, C:T.144, C:N.145, C:N.145, C:N.145, C:Q.168 NAD.7: 26 residues within 4Å: Chain D: I.31, G.32, A.33, G.34, F.35, T.36, V.55, D.56, I.57, L.60, Y.90, T.102, A.103, G.104, I.123, Q.126, V.127, L.143, T.144, N.145, Q.168, L.172, H.200, A.250, P.254 Ligands: OAA.8 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:L.143, D:L.172, D:P.254 Hydrogen bonds: D:G.32, D:A.33, D:G.34, D:F.35, D:T.36, D:T.36, D:Y.90, D:G.104, D:Q.126, D:L.143, D:N.145, D:N.145, D:Q.168

4 x OAA: OXALOACETATE ION(Non-covalent)

OAA.2: 9 residues within 4Å: Chain A: N.145, L.172, R.176, H.200, G.238, V.242, S.249, A.250 Ligands: NAD.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.145 Salt bridges: A:R.176, A:H.200 OAA.4: 7 residues within 4Å: Chain B: N.145, L.172, R.176, H.200, G.238, G.239 Ligands: NAD.3 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.145, B:G.238 Salt bridges: B:R.176, B:H.200 OAA.6: 8 residues within 4Å: Chain C: N.145, L.172, R.176, H.200, G.238, S.249, A.250 Ligands: NAD.5 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.145, C:S.249 Salt bridges: C:R.176, C:H.200 OAA.8: 8 residues within 4Å: Chain D: N.145, L.172, R.176, H.200, G.238, S.249, A.250 Ligands: NAD.7 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.145 Salt bridges: D:R.176, D:H.200

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shimozawa, Y. et al., Structural analysis and reaction mechanism of malate dehydrogenase from Geobacillus stearothermophilus. J.Biochem. (2021)

Release Date

2021-03-24

Peptides

Malate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Malate dehydrogenase

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