SMTL ID : 9c0p.1 (1 other biounit)

M. tuberculosis PKS13 acyltransferase (AT) domain in complex with SuFEx inhibitor CEC215

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

monomer

Ligands

3 x GLC- FRU: beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose(Non-covalent)

GLC-FRU.1: 9 residues within 4Å: Chain A: R.55, L.56, A.59, E.63, K.177, L.210, D.211, D.212, A.213 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:E.63, A:R.55, A:R.55, A:D.211, A:D.211, A:D.212, A:D.212, A:A.213 Water bridges: A:A.60, A:K.177, A:K.177 GLC-FRU.2: 12 residues within 4Å: Chain A: H.119, R.123, L.481, Y.482, G.485, H.486, D.487, L.488, D.489, I.490, R.491 Ligands: 1PE.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.123, A:R.123, A:L.481, A:L.488, A:L.488, A:D.489, A:I.490, A:R.491, A:R.491 Water bridges: A:H.119, A:G.120, A:D.487, A:D.487, A:R.491 GLC-FRU.3: 4 residues within 4Å: Chain A: E.289, P.312, P.330, Q.333 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.333, A:E.289, A:Q.333 Water bridges: A:E.332

6 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.4: 14 residues within 4Å: Chain A: F.168, M.279, G.282, E.283, M.285, L.286, M.294, T.353, G.355, S.357, Q.361, M.362, L.365 Ligands: 01.13 No protein-ligand interaction detected (PLIP) 1PE.5: 11 residues within 4Å: Chain A: G.120, R.121, R.123, V.153, D.154, G.155, P.156, V.483, Y.484, G.485 Ligands: GLC-FRU.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.483 1PE.6: 4 residues within 4Å: Chain A: S.264, R.266, D.267, K.377 No protein-ligand interaction detected (PLIP) 1PE.7: 3 residues within 4Å: Chain A: A.188, W.189, K.192 No protein-ligand interaction detected (PLIP) 1PE.8: 3 residues within 4Å: Chain A: H.277, E.281, E.372 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.368 1PE.9: 3 residues within 4Å: Chain A: Y.203, E.219, T.220 No protein-ligand interaction detected (PLIP)

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.10: 4 residues within 4Å: Chain A: P.507, P.508, T.509, R.510 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.510 SO4.11: 6 residues within 4Å: Chain A: E.92, L.93, W.96, R.117, I.506, P.507 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.92 Water bridges: A:L.93, A:R.117 Salt bridges: A:R.117 SO4.12: 2 residues within 4Å: Chain A: T.492, L.493 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.239

1 x 01: N-{4-[(4-{[fluorodi(hydroxy)-lambda~4~-sulfanyl]oxy}phenoxy)methyl]phenyl}acetamide

01.13: 16 residues within 4Å: Chain A: F.168, Q.222, Q.249, S.250, L.251, R.275, M.279, M.294, L.296, V.318, V.326, R.349, S.357, H.358, Q.445 Ligands: 1PE.4 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.168, A:L.296, A:V.318, A:V.326 Hydrogen bonds: A:Q.222, A:R.349, A:R.349, A:S.357 pi-Stacking: A:F.168, A:F.351

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Krieger, I.K. et al., A SuFEx-based TB clinical candidate irreversibly inhibits Pks13. To Be Published

Release Date

2025-05-07

Peptides

Polyketide synthase Pks13: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Polyketide synthase Pks13

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