SMTL ID : 4ncr.1 (1 other biounit)

Crystal structure of M. tuberculosis DprE1 in complex with PBTZ169

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

monomer

Ligands

1 x 26J: 2-(4-(cyclohexylmethyl)piperazin-1-yl)-8-nitro-6-(trifluoromethyl)-4H-benzo[e][1,3]thiazin-4-one, bound form(Covalent)

26J.1: 12 residues within 4Å: Chain A: G.137, H.152, G.153, K.154, S.248, V.385, K.387, F.389, N.405, C.407, K.438 Ligands: FAD.2 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.385 Hydrogen bonds: A:K.154, A:K.438 Water bridges: A:Q.356, A:Q.356, A:K.438 Halogen bonds: A:N.405

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

FAD.2: 33 residues within 4Å: Chain A: W.36, I.72, A.73, R.74, G.75, L.76, G.77, R.78, S.79, Y.80, N.83, A.84, M.94, A.114, P.136, G.137, T.138, V.141, T.142, G.144, G.145, A.148, C.149, I.151, H.152, N.198, G.199, G.202, I.203, I.204, Y.435, A.437 Ligands: 26J.1 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:W.36, A:R.78, A:Y.80, A:T.138 Hydrogen bonds: A:G.75, A:L.76, A:G.77, A:R.78, A:S.79, A:S.79, A:N.83, A:G.137, A:T.142, A:T.142, A:G.145, A:H.152, A:H.152, A:N.198, A:I.204, A:I.204, A:Y.435 Water bridges: A:G.144, A:G.144, A:Q.356, A:K.438 pi-Cation interactions: A:K.438

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: W.250, F.251, D.252, R.262, A.264, Y.317 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.262, A:A.264, A:Y.317 Water bridges: A:F.251 GOL.4: 5 residues within 4Å: Chain A: S.102, D.104, T.107, L.109, T.208 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.102, A:S.102, A:T.107, A:T.208 GOL.5: 1 residues within 4Å: Chain A: A.242 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Makarov, V. et al., Towards a new combination therapy for tuberculosis with next generation benzothiazinones. EMBO Mol Med (2014)

Release Date

2014-02-19

Peptides

decaprenylphosphoryl-beta-D-ribose oxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

decaprenylphosphoryl-beta-D-ribose oxidase

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