SMTL ID : 9c9o.1 (1 other biounit)

M. tuberculosis PKS13 acyltransferase (AT) domain in complex with SuFEx inhibitor CMX410 - reaction product

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.02 Å

Oligo State

monomer

Ligands

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

GLC-FRU.1: 8 residues within 4Å: Chain A: R.55, L.56, E.63, K.177, L.210, D.211, D.212, A.213 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:E.63, A:R.55, A:R.55, A:K.177, A:D.211, A:D.211, A:D.212, A:D.212, A:A.213 GLC-FRU.2: 10 residues within 4Å: Chain A: H.119, R.123, Y.482, G.485, H.486, D.487, L.488, D.489, I.490, R.491 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.123, A:R.123, A:L.481, A:G.485, A:L.488, A:L.488, A:D.489, A:I.490, A:R.491 Water bridges: A:D.487

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

SO4.3: 5 residues within 4Å: Chain A: I.506, P.507, P.508, T.509, R.510 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.510 SO4.4: 6 residues within 4Å: Chain A: E.92, L.93, R.117, I.506, P.507, R.510 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.92, A:R.510 Water bridges: A:L.93, A:L.93 Salt bridges: A:R.117

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

1PE.5: 12 residues within 4Å: Chain A: M.279, G.282, E.283, L.286, T.353, G.355, A.356, S.357, Q.361, M.362, P.364, L.365 No protein-ligand interaction detected (PLIP) 1PE.6: 6 residues within 4Å: Chain A: F.168, G.169, Q.171, Y.216, G.217, T.221 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.171, A:Y.216 Water bridges: A:R.173

1 x 02: 4-({2,6-difluoro-4-[3-(methanesulfonamido)-1H-1,2,4-triazol-1-yl]phenyl}methoxy)phenyl hydrogen sulfate

02.7: 17 residues within 4Å: Chain A: F.168, Q.249, X.250, R.275, M.294, L.296, V.318, A.320, Q.324, V.326, R.349, F.351, S.357, H.358, V.416, V.441, Q.445 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.168, A:L.296, A:V.318, A:V.326, A:F.351 Hydrogen bonds: A:R.275, A:R.349, A:S.357, A:S.357 Water bridges: A:F.168, A:Q.324 Salt bridges: A:H.358 pi-Stacking: A:F.168

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Krieger, I.V. 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