SMTL ID : 7kmy.1 (3 other biounits)

Structure of Mtb Lpd bound to 010705

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.21 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 37 residues within 4Å: Chain A: L.11, G.12, G.14, P.15, G.16, V.34, E.35, P.36, K.37, Y.38, G.41, V.42, C.43, V.46, G.47, C.48, S.51, K.52, Y.114, G.115, A.143, T.144, G.145, Y.163, I.184, Y.278, G.310, D.311, Q.317, L.318, A.319, H.320, A.322, F.352 Chain B: H.445, P.446 Ligands: GOL.5 19 PLIP interactions: 18 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.42, A:Y.163, A:I.184 Hydrogen bonds: A:G.14, A:G.16, A:V.42, A:C.43, A:K.52, A:G.115, A:G.115, A:D.311, A:Q.317, A:A.319, B:H.445 Water bridges: A:G.145, A:S.146, A:S.146, A:S.146, A:V.312 FAD.9: 37 residues within 4Å: Chain A: H.445, P.446 Chain B: L.11, G.12, G.14, P.15, G.16, V.34, E.35, P.36, Y.38, G.41, V.42, C.43, V.46, G.47, C.48, K.52, Y.114, G.115, A.143, T.144, G.145, Y.163, I.184, F.188, Y.278, G.310, D.311, Q.317, L.318, A.319, H.320, A.322, F.352 Ligands: GOL.13, GOL.14 20 PLIP interactions: 19 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.163, B:I.184, B:F.188 Hydrogen bonds: B:G.14, B:G.16, B:V.42, B:C.43, B:K.52, B:G.115, B:G.115, B:D.311, B:Q.317, B:A.319, B:H.320, A:H.445 Water bridges: B:G.145, B:S.146, B:S.146, B:S.146, B:V.312

2 x WPM: N~2~-methyl-N~2~-[(5-methyl-1H-indazol-7-yl)sulfonyl]-N-(1-methyl-2-oxo-1,2-dihydropyridin-4-yl)glycinamide(Non-covalent)

WPM.2: 14 residues within 4Å: Chain A: Y.18, L.44, R.95, G.98, V.99, F.101, E.323 Chain B: A.383, N.384, A.385, H.445, E.450, N.465, F.466 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:F.466 Hydrogen bonds: B:A.383, B:N.465, A:R.95 Water bridges: B:N.384, B:A.385, B:A.385, A:R.95, A:R.95 WPM.3: 14 residues within 4Å: Chain A: A.383, N.384, A.385, H.445, E.450, N.465, F.466 Chain B: Y.18, L.44, R.95, G.98, V.99, F.101, E.323 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.466 Hydrogen bonds: A:A.383, A:N.465, B:R.95 Water bridges: A:N.384, A:H.445, A:H.445, B:R.95

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: Q.453, E.454, H.457, I.464, N.465 Chain B: E.323, A.324 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Water bridges: B:E.323, B:E.323, B:E.323, B:A.324 Hydrogen bonds: A:Q.453, A:E.454, A:N.465 GOL.5: 7 residues within 4Å: Chain A: K.52, A.183, I.184, E.187, L.318, A.350 Ligands: FAD.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.52, A:A.350, A:A.350 Water bridges: A:Q.317 GOL.6: 6 residues within 4Å: Chain A: S.147, A.272, P.273, N.274, V.275, E.276 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.147, A:N.274, A:V.275, A:E.276 GOL.7: 4 residues within 4Å: Chain A: V.295, D.296, D.297, L.315 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.295, A:D.297, A:D.297 Water bridges: A:V.295, A:H.344 GOL.8: 3 residues within 4Å: Chain A: Q.365, Q.366, N.369 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.369, A:N.369 GOL.10: 8 residues within 4Å: Chain A: E.323, A.324, V.327 Chain B: Q.453, E.454, H.457, I.464, N.465 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.453, B:Q.453, B:N.465 Water bridges: B:H.443, A:A.324 GOL.11: 6 residues within 4Å: Chain B: G.180, A.181, G.182, E.203, L.205, I.269 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.181, B:G.182 Water bridges: B:F.204, B:F.204 GOL.12: 8 residues within 4Å: Chain A: K.386 Chain B: K.52, L.55, R.56, E.59, F.352, Q.354, N.356 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:K.386, B:K.52, B:R.56, B:Q.354, B:N.356 GOL.13: 9 residues within 4Å: Chain B: K.37, Y.38, V.42, S.146, S.147, Y.163, E.164, N.274 Ligands: FAD.9 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.147, B:E.164, B:N.274 Water bridges: B:T.144, B:S.146 GOL.14: 8 residues within 4Å: Chain B: K.52, A.183, I.184, E.187, L.318, A.350, F.352 Ligands: FAD.9 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.52 Water bridges: B:A.350 GOL.15: 4 residues within 4Å: Chain B: Y.85, R.89, E.93, L.168 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.85, B:R.89, B:R.89, B:E.93 GOL.16: 5 residues within 4Å: Chain A: R.87 Chain B: D.67, A.70, F.71, G.391 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.87, B:D.67 Water bridges: B:D.67

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ginn, J. et al., Whole Cell Active Inhibitors of Mycobacterial Lipoamide Dehydrogenase Afford Selectivity over the Human Enzyme through Tight Binding Interactions. Acs Infect Dis. (2021)

Release Date

2021-01-27

Peptides

Dihydrolipoyl dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dihydrolipoyl dehydrogenase

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