SMTL ID : 5z20.2 (1 other biounit)

The ternary structure of D-lactate dehydrogenase from Pseudomonas aeruginosa with NADH and oxamate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

4 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.1: 23 residues within 4Å: Chain A: Y.116, V.121, G.167, T.168, G.169, Q.170, I.171, Y.189, D.190, P.191, Y.192, H.220, C.221, P.222, T.227, T.248, G.249, R.250, D.274, H.311, A.313, F.314 Ligands: OXM.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:V.121, A:I.171 Hydrogen bonds: A:Q.170, A:Q.170, A:I.171, A:D.274, A:D.274, A:A.313, A:F.314 Water bridges: A:N.96, A:G.169, A:G.172, A:L.223 NAI.4: 24 residues within 4Å: Chain B: P.114, Y.116, V.121, G.167, G.169, Q.170, I.171, Y.189, D.190, P.191, Y.192, H.220, C.221, P.222, T.227, T.248, G.249, R.250, D.274, V.275, H.311, A.313, F.314 Ligands: OXM.5 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:V.121, B:I.171 Hydrogen bonds: B:Q.170, B:Q.170, B:I.171, B:D.274, B:D.274, B:A.313, B:F.314 Water bridges: B:N.96, B:T.168, B:G.169, B:G.172, B:L.223, B:L.223, B:L.223 NAI.7: 23 residues within 4Å: Chain C: Y.116, V.121, G.167, T.168, G.169, Q.170, I.171, Y.189, D.190, P.191, Y.192, H.220, C.221, P.222, T.227, T.248, G.249, R.250, D.274, H.311, A.313, F.314 Ligands: OXM.8 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:V.121, C:I.171 Hydrogen bonds: C:Q.170, C:Q.170, C:I.171, C:D.274, C:A.313, C:F.314 Water bridges: C:N.96, C:G.169, C:G.172, C:L.223 NAI.10: 24 residues within 4Å: Chain D: P.114, Y.116, V.121, G.167, G.169, Q.170, I.171, Y.189, D.190, P.191, Y.192, H.220, C.221, P.222, T.227, T.248, G.249, R.250, D.274, V.275, H.311, A.313, F.314 Ligands: OXM.11 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:V.121, D:I.171 Hydrogen bonds: D:Q.170, D:Q.170, D:I.171, D:D.274, D:A.313, D:F.314 Water bridges: D:N.96, D:G.169, D:G.172, D:L.223, D:L.223, D:L.223

4 x OXM: OXAMIC ACID(Non-covalent)

OXM.2: 10 residues within 4Å: Chain A: F.67, V.68, S.92, A.93, G.94, Y.116, R.250, H.311, F.314 Ligands: NAI.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:A.93, A:G.94, A:Y.116, A:R.250, A:R.250, A:H.311 Salt bridges: A:R.250 OXM.5: 10 residues within 4Å: Chain B: F.67, V.68, S.92, A.93, G.94, Y.116, R.250, H.311, F.314 Ligands: NAI.4 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:A.93, B:G.94, B:Y.116, B:R.250, B:R.250, B:H.311 Salt bridges: B:R.250 OXM.8: 10 residues within 4Å: Chain C: F.67, V.68, S.92, A.93, G.94, Y.116, R.250, H.311, F.314 Ligands: NAI.7 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:A.93, C:G.94, C:Y.116, C:Y.116, C:R.250, C:R.250, C:H.311 Salt bridges: C:R.250 OXM.11: 10 residues within 4Å: Chain D: F.67, V.68, S.92, A.93, G.94, Y.116, R.250, H.311, F.314 Ligands: NAI.10 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:A.93, D:G.94, D:Y.116, D:Y.116, D:R.250, D:R.250, D:H.311 Salt bridges: D:R.250

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.3: 5 residues within 4Å: Chain A: S.73, N.96, H.97, V.98, D.99 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.73 PG4.9: 5 residues within 4Å: Chain C: S.73, N.96, H.97, V.98, D.99 1 PLIP interactions: 1 interactions with chain C Water bridges: C:S.73

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.6: 4 residues within 4Å: Chain B: N.96, H.97, V.98, D.99 No protein-ligand interaction detected (PLIP) PGE.12: 4 residues within 4Å: Chain D: N.96, H.97, V.98, D.99 1 PLIP interactions: 1 interactions with chain D Water bridges: D:D.99

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Furukawa, N. et al., Structural Basis of Sequential Allosteric Transitions in Tetrameric d-Lactate Dehydrogenases from Three Gram-Negative Bacteria. Biochemistry (2018)

Release Date

2018-09-19

Peptides

D-lactate dehydrogenase (Fermentative): ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
E

D
F

D-lactate dehydrogenase (Fermentative)

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