SMTL ID : 5u8v.2 (1 other biounit)

Dihydrolipoamide dehydrogenase (LpdG) from Pseudomonas aeruginosa bound to NAD+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 44 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, L.199, R.282, V.285, 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.7 29 PLIP interactions: 26 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:T.51, A:I.195 Hydrogen bonds: A:A.15, 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:K.38, A:G.155, A:V.323, A:A.333, B:H.454, B:H.454 FAD.12: 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.16 25 PLIP interactions: 22 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:I.195 Hydrogen bonds: B:G.16, B:G.18, 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, B:H.331, A:H.454 Water bridges: B:G.19, B:G.155, B:S.156, B:V.323, A:H.454, A:H.454

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

NAD.2: 19 residues within 4Å: Chain A: I.161, I.190, G.191, A.192, G.193, V.194, I.195, G.196, L.213, E.214, A.215, L.216, A.246, R.247, V.248, A.279, V.280, G.281, R.282 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.193, A:I.195, A:A.215, A:V.248, A:V.248, A:G.281 Water bridges: A:V.194, A:G.196, A:G.196, A:G.281, A:R.282 NAD.13: 19 residues within 4Å: Chain B: I.161, I.190, G.191, A.192, G.193, V.194, I.195, G.196, L.213, E.214, A.215, L.216, A.246, R.247, V.248, A.279, V.280, G.281, R.282 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:G.193, B:I.195, B:E.214, B:A.215, B:R.247, B:V.248, B:V.248, B:A.279, B:G.281 Water bridges: B:V.194, B:V.194, B:G.196, B:G.196, B:R.247, B:R.247, B:R.282

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

DMS.3: 5 residues within 4Å: Chain A: N.400, D.401, T.402, T.403 Ligands: DMS.5 Ligand excluded by PLIP DMS.4: 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.17 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.3 Ligand excluded by PLIP DMS.6: 8 residues within 4Å: Chain A: G.386, T.387, F.388, A.467, I.475, A.476, N.477, R.478 Ligand excluded by PLIP DMS.7: 6 residues within 4Å: Chain A: Y.39, G.50, T.51, N.54, V.55 Ligands: FAD.1 Ligand excluded by PLIP DMS.8: 11 residues within 4Å: Chain A: P.17, Y.20, V.21, C.52, A.330, H.331, S.334 Chain B: H.454, E.459, H.474 Ligands: DMS.19 Ligand excluded by PLIP DMS.9: 5 residues within 4Å: Chain A: D.217, K.218, F.219, L.232, L.244 Ligand excluded by PLIP DMS.10: 4 residues within 4Å: Chain A: L.232, I.242, R.243, L.244 Ligand excluded by PLIP DMS.11: 6 residues within 4Å: Chain A: A.215, L.216, D.217, K.218, G.245, R.247 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: 8 residues within 4Å: Chain A: K.69 Chain B: Y.68, E.72, A.76, H.363, A.399, N.400, D.401 Ligand excluded by PLIP DMS.16: 7 residues within 4Å: Chain B: Y.39, G.50, T.51, N.54, V.55, S.156 Ligands: FAD.12 Ligand excluded by PLIP DMS.17: 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.4 Ligand excluded by PLIP DMS.18: 9 residues within 4Å: Chain B: G.386, T.387, F.388, P.389, A.467, A.472, I.475, A.476, N.477 Ligand excluded by PLIP DMS.19: 11 residues within 4Å: Chain A: Y.20 Chain B: F.388, A.392, S.393, G.394, R.395, H.454, E.459, E.463, H.474 Ligands: DMS.8 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

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
C

B
D

Dihydrolipoyl dehydrogenase

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