SMTL ID : 4prl.1

Crystal structure of D-lactate dehydrogenase with NAD+ from Lactobacillus jensenii

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 22 residues within 4Å: Chain A: Y.101, I.106, I.152, G.153, V.154, G.155, H.156, I.157, Y.175, D.176, V.177, H.205, T.206, P.207, T.212, A.233, A.234, R.235, D.259, H.295, A.297, Y.298 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:I.106 Hydrogen bonds: A:G.155, A:H.156, A:I.157, A:G.158, A:D.176, A:T.206, A:D.259, A:D.259, A:A.297, A:Y.298 Water bridges: A:R.235, A:R.235 NAD.2: 22 residues within 4Å: Chain B: Y.101, I.106, G.153, V.154, G.155, H.156, I.157, G.158, Y.175, D.176, V.177, H.205, T.206, P.207, T.212, A.233, A.234, R.235, D.259, H.295, A.297, Y.298 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:I.106 Hydrogen bonds: B:V.154, B:G.155, B:H.156, B:I.157, B:G.158, B:D.259, B:H.295, B:Y.298 Water bridges: B:L.208, B:L.208 NAD.3: 22 residues within 4Å: Chain C: Y.101, I.106, I.152, G.153, V.154, G.155, H.156, I.157, Y.175, D.176, V.177, H.205, T.206, P.207, T.212, A.233, A.234, R.235, D.259, H.295, A.297, Y.298 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:I.106 Hydrogen bonds: C:G.155, C:H.156, C:I.157, C:G.158, C:T.206, C:T.206, C:D.259, C:H.295, C:A.297, C:Y.298 Water bridges: C:R.235, C:R.235 NAD.4: 22 residues within 4Å: Chain D: Y.101, I.106, G.153, V.154, G.155, H.156, I.157, G.158, Y.175, D.176, V.177, H.205, T.206, P.207, T.212, A.233, A.234, R.235, D.259, H.295, A.297, Y.298 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:I.106 Hydrogen bonds: D:V.154, D:G.155, D:H.156, D:I.157, D:G.158, D:D.176, D:D.259, D:D.259, D:Y.298 Water bridges: D:L.208, D:L.208

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, S. et al., Crystal structure and thermodynamic properties of d-lactate dehydrogenase from Lactobacillus jensenii. Int.J.Biol.Macromol. (2014)

Release Date

2014-06-18

Peptides

4-phosphoerythronate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

4-phosphoerythronate dehydrogenase

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