SMTL ID : 8ct4.1

Cryo-EM structure of Mtb Lpd bound to inhibitor complex with 2-((2-cyano-N,5-dimethyl-1H-indole)-7-sulfonamido)-N-(4-(oxetan-3-yl)-3,4-dihydro-2H-benzo[b] [1,4]oxazin-7-yl)acetamide

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

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

FAD.1: 44 residues within 4Å: Chain A: L.11, G.12, A.13, G.14, P.15, G.16, G.17, 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, G.113, Y.114, G.115, A.143, T.144, G.145, S.146, Y.163, I.167, I.184, F.188, F.271, N.274, Y.278, G.310, D.311, Q.317, L.318, A.319, H.320, A.322, F.352 Chain B: H.445, P.446 26 PLIP interactions: 25 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.42, A:Y.163, A:I.184, A:I.184, A:F.271 Hydrogen bonds: A:A.13, A:G.14, A:G.16, A:E.35, A:E.35, A:V.42, A:C.43, A:K.52, A:G.115, A:G.115, A:D.311, A:D.311, A:A.319, B:H.445 Water bridges: A:G.17, A:G.17, A:G.145, A:S.146, A:S.146, A:S.146, A:I.309 FAD.4: 44 residues within 4Å: Chain A: H.445, P.446 Chain B: L.11, G.12, A.13, G.14, P.15, G.16, G.17, 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, G.113, Y.114, G.115, A.143, T.144, G.145, S.146, Y.163, I.167, I.184, F.188, F.271, N.274, Y.278, G.310, D.311, Q.317, L.318, A.319, H.320, A.322, F.352 26 PLIP interactions: 25 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.42, B:Y.163, B:I.184, B:I.184, B:F.271 Hydrogen bonds: B:A.13, B:G.14, B:G.16, B:E.35, B:E.35, B:V.42, B:C.43, B:K.52, B:G.115, B:G.115, B:D.311, B:D.311, B:A.319, A:H.445 Water bridges: B:G.17, B:G.17, B:G.145, B:S.146, B:S.146, B:S.146, B:I.309

2 x OU6: N~2~-(2-cyano-5-methyl-1H-indole-7-sulfonyl)-N~2~-methyl-N-[4-(oxetan-3-yl)-3,4-dihydro-2H-1,4-benzoxazin-7-yl]glycinamide(Non-covalent)

OU6.2: 22 residues within 4Å: Chain A: P.15, Y.18, C.43, L.44, R.95, G.98, V.99, F.101, L.102, A.319, E.323 Chain B: F.379, T.382, A.383, N.384, A.385, H.445, E.450, A.451, E.454, N.465, F.466 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:P.15, A:F.101, B:A.383 Hydrogen bonds: A:R.95, A:R.95, B:A.383, B:N.384, B:N.465 Water bridges: B:A.385 OU6.3: 22 residues within 4Å: Chain A: F.379, T.382, A.383, N.384, A.385, H.445, E.450, A.451, E.454, N.465, F.466 Chain B: P.15, Y.18, C.43, L.44, R.95, G.98, V.99, F.101, L.102, A.319, E.323 9 PLIP interactions: 4 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:P.15, B:F.101, A:A.383 Hydrogen bonds: B:R.95, B:R.95, A:A.383, A:N.384, A:N.465 Water bridges: A:A.385

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kochanczyk, T. et al., Cryo-EM structure of Mtb Lpd bound to the inhibitor 2-((2-cyano-N,5-dimethyl-1H-indole)-7-sulfonamido)-N-(4-(oxetan-3-yl)-3,4-dihydro-2H-benzo[b] [1,4]oxazin-7-yl)acetamide at 2.17 Angstrom resolution. Not published

Release Date

2022-05-25

Peptides

Dihydrolipoyl dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dihydrolipoyl dehydrogenase

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