SMTL ID : 5u8u.1 (1 other biounit)

Dihydrolipoamide dehydrogenase (LpdG) from Pseudomonas aeruginosa

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

homo-dimer

Ligands

2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.1: 46 residues within 4Å: Chain A: I.13, G.14, A.15, G.16, P.17, G.18, G.19, I.36, E.37, K.38, Y.39, G.50, T.51, C.52, V.55, G.56, C.57, S.60, K.61, G.123, H.124, G.125, A.153, S.154, G.155, S.156, S.174, L.178, I.195, E.198, L.199, R.282, V.285, T.287, L.289, G.321, D.322, M.328, L.329, A.330, H.331, A.333, Y.361 Chain B: H.454, P.455 Ligands: DMS.4 27 PLIP interactions: 24 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:T.51, A:I.195 Hydrogen bonds: A:G.16, A:G.18, A:G.19, A:E.37, A:K.38, A:Y.39, A:G.50, A:T.51, A:T.51, A:T.51, A:C.52, A:K.61, A:G.125, A:G.125, A:S.156, A:D.322, A:L.329, A:A.330, A:H.331, B:H.454 Water bridges: A:G.155, A:S.156, A:V.323, B:H.454, B:H.454 FAD.10: 44 residues within 4Å: Chain A: H.454, P.455 Chain B: I.13, G.14, A.15, G.16, P.17, G.18, G.19, I.36, E.37, K.38, Y.39, G.50, T.51, C.52, V.55, G.56, C.57, S.60, K.61, G.123, H.124, G.125, A.153, S.154, G.155, S.156, S.174, L.178, I.195, L.199, R.282, V.285, L.289, G.321, D.322, M.328, L.329, A.330, H.331, A.333, Y.361 Ligands: DMS.11 25 PLIP interactions: 22 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:T.51, B:I.195 Hydrogen bonds: B:G.16, B:G.18, B:G.19, B:E.37, B:K.38, B:G.50, B:T.51, B:T.51, B:T.51, B:C.52, B:K.61, B:G.125, B:G.125, B:S.156, B:D.322, B:L.329, B:A.330, A:H.454 Water bridges: B:G.155, B:S.156, B:V.323, A:H.454, A:H.454

19 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.2: 5 residues within 4Å: Chain A: N.400, D.401, T.402, T.403 Ligands: DMS.5 Ligand excluded by PLIP DMS.3: 5 residues within 4Å: Chain A: A.327, L.329, I.356, P.357, S.358 Ligand excluded by PLIP DMS.4: 7 residues within 4Å: Chain A: Y.39, G.50, T.51, N.54, V.55, S.156 Ligands: FAD.1 Ligand excluded by PLIP DMS.5: 10 residues within 4Å: Chain A: Y.68, H.71, E.72, A.76, H.363, A.399, N.400, D.401 Chain B: K.69 Ligands: DMS.2 Ligand excluded by PLIP DMS.6: 11 residues within 4Å: Chain A: F.388, A.392, S.393, G.394, R.395, H.454, E.459, E.463, H.474 Chain B: L.105 Ligands: DMS.9 Ligand excluded by PLIP DMS.7: 5 residues within 4Å: Chain A: D.217, K.218, F.219, L.232, L.244 Ligand excluded by PLIP DMS.8: 9 residues within 4Å: Chain A: P.17, Y.20, V.21, A.330, H.331, S.334 Chain B: H.454, E.459, H.474 Ligand excluded by PLIP DMS.9: 10 residues within 4Å: Chain A: H.454, E.459, H.474 Chain B: P.17, Y.20, V.21, A.330, H.331, S.334 Ligands: DMS.6 Ligand excluded by PLIP DMS.11: 7 residues within 4Å: Chain B: Y.39, G.50, T.51, N.54, V.55, S.156 Ligands: FAD.10 Ligand excluded by PLIP DMS.12: 5 residues within 4Å: Chain B: N.400, D.401, T.402, T.403 Ligands: DMS.13 Ligand excluded by PLIP DMS.13: 10 residues within 4Å: Chain A: K.69 Chain B: Y.68, H.71, E.72, A.76, H.363, A.399, N.400, D.401 Ligands: DMS.12 Ligand excluded by PLIP DMS.14: 6 residues within 4Å: Chain B: P.162, P.163, A.164, P.165, A.250, S.251 Ligand excluded by PLIP DMS.15: 6 residues within 4Å: Chain B: A.327, L.329, I.356, P.357, S.358, W.368 Ligand excluded by PLIP DMS.16: 6 residues within 4Å: Chain B: G.386, T.387, A.467, I.475, A.476, N.477 Ligand excluded by PLIP DMS.17: 10 residues within 4Å: Chain A: L.105 Chain B: F.388, A.392, S.393, G.394, R.395, H.454, E.459, E.463, H.474 Ligand excluded by PLIP DMS.18: 2 residues within 4Å: Chain B: D.307, D.308 Ligand excluded by PLIP DMS.19: 7 residues within 4Å: Chain B: Y.70, T.88, I.89, V.91, V.183, L.206, G.207 Ligand excluded by PLIP DMS.20: 5 residues within 4Å: Chain B: D.217, K.218, F.219, L.232, L.244 Ligand excluded by PLIP DMS.21: 5 residues within 4Å: Chain B: A.215, L.216, D.217, K.218, G.245 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Glasser, N.R. et al., The Pyruvate and alpha-Ketoglutarate Dehydrogenase Complexes of Pseudomonas aeruginosa Catalyze Pyocyanin and Phenazine-1-carboxylic Acid Reduction via the Subunit Dihydrolipoamide Dehydrogenase. J. Biol. Chem. (2017)

Release Date

2017-02-15

Peptides

Dihydrolipoyl dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dihydrolipoyl dehydrogenase

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