SMTL ID : 7c2m.1

Crystal structure of mycolic acid transporter MmpL3 from Mycobacterium smegmatis complexed with NITD-349

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

monomer

Ligands

1 x FFU: N-(4,4-dimethylcyclohexyl)-4,6-bis(fluoranyl)-1H-indole-2-carboxamide(Non-covalent)

FFU.1: 12 residues within 4Å: Chain A: I.254, I.258, D.261, F.265, I.302, V.643, G.646, L.647, D.650, Y.651, F.654, L.691 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:I.258, A:I.258, A:D.261, A:F.265, A:I.302, A:V.643, A:L.647, A:F.654, A:F.654, A:L.691 Hydrogen bonds: A:D.650, A:D.650, A:D.650

5 x L6T: alpha-D-glucopyranosyl 6-O-dodecyl-alpha-D-glucopyranoside(Non-covalent)

L6T.2: 8 residues within 4Å: Chain A: Q.2, F.7, R.293, T.294, V.296, F.297, S.657, E.661 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.2, A:R.293, A:R.293, A:R.293, A:S.657, A:E.661 Salt bridges: A:R.293 L6T.3: 16 residues within 4Å: Chain A: Q.45, F.48, Y.49, V.56, S.59, L.60, D.63, R.68, D.69, D.149, L.176, A.180, H.244, F.245, I.432, R.506 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.48, A:A.180, A:F.245 Hydrogen bonds: A:S.59, A:D.63, A:R.68, A:D.69, A:D.69, A:D.149, A:R.506 Salt bridges: A:R.68 L6T.4: 13 residues within 4Å: Chain A: T.71, S.72, V.75, D.124, T.126, V.127, M.130, F.139, L.176, Q.447, F.450, F.457, R.458 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.139, A:L.176, A:F.450, A:F.457 Hydrogen bonds: A:T.126 L6T.5: 6 residues within 4Å: Chain A: G.619, H.620, G.621, L.624, M.625 Ligands: L6T.6 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.624 Hydrogen bonds: A:H.620, A:G.621 L6T.6: 4 residues within 4Å: Chain A: D.440, N.626, F.700 Ligands: L6T.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.193, A:D.440, A:N.626

2 x MHA: (CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC ACID(Non-covalent)

MHA.7: 8 residues within 4Å: Chain A: D.764, T.896, P.897, N.898, R.899, I.922, K.923, A.924 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.898, A:R.899, A:K.923, A:A.924 Salt bridges: A:R.899 MHA.8: 6 residues within 4Å: Chain A: G.867, F.868, T.869, N.870, S.871, N.886 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.869, A:S.871, A:N.886, A:N.886, A:N.886

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, X. et al., Structural Basis for the Inhibition of Mycobacterial MmpL3 by NITD-349 and SPIRO. J.Mol.Biol. (2020)

Release Date

2020-12-02

Peptides

Chimera of drug exporters of the RND superfamily-like protein and Endolysin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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Chimera of drug exporters of the RND superfamily-like protein and Endolysin

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