SMTL ID : 9c1d.1 (1 other biounit)

Mycobaterium tuberculosis Pks13 acyltransferase incubated with DMSO

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

monomer

Ligands

3 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.1: 7 residues within 4Å: Chain A: F.147, Q.228, L.275, V.305, F.330, V.420, Q.424 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.424 Water bridges: A:A.421 DMS.16: 3 residues within 4Å: Chain A: L.61, T.62, S.63 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.63 DMS.18: 1 residues within 4Å: Chain A: Q.125 No protein-ligand interaction detected (PLIP)

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

SO4.2: 9 residues within 4Å: Chain A: F.147, Q.201, S.229, L.230, R.254, M.258, S.336, H.337 Ligands: PE5.8 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.229, A:L.230, A:S.336 Water bridges: A:S.229, A:S.229 Salt bridges: A:R.254, A:H.337 SO4.3: 4 residues within 4Å: Chain A: P.486, P.487, T.488, R.489 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.487, A:R.489 SO4.4: 3 residues within 4Å: Chain A: D.109, H.110 Ligands: EDO.19 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.110 Water bridges: A:L.86, A:D.109, A:D.111 Salt bridges: A:H.110 SO4.5: 4 residues within 4Å: Chain A: Y.237, S.243, L.244 Ligands: SO4.6 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.244 Water bridges: A:Y.237, A:Y.237, A:S.243, A:R.245 SO4.6: 5 residues within 4Å: Chain A: S.243, R.245, D.246, K.356 Ligands: SO4.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.243 Water bridges: A:S.243, A:S.243, A:R.245 Salt bridges: A:K.356 SO4.7: 6 residues within 4Å: Chain A: E.71, W.75, R.96, I.485, P.486, R.489 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.96 Water bridges: A:L.72, A:W.75 Salt bridges: A:R.489

1 x PE5: 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL(Non-covalent)

PE5.8: 18 residues within 4Å: Chain A: F.147, Q.150, I.197, Q.201, M.258, G.261, E.262, M.273, F.330, A.331, T.332, G.334, A.335, S.336, Q.340, M.341, L.344 Ligands: SO4.2 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.331 Hydrogen bonds: A:Q.150, A:Q.201

10 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.9: 4 residues within 4Å: Chain A: H.151, R.152, K.153, R.445 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.152, A:R.152, A:K.153 EDO.10: 4 residues within 4Å: Chain A: H.151, A.444, Q.447, E.449 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.449 Water bridges: A:S.157, A:A.444 EDO.11: 3 residues within 4Å: Chain A: L.43, S.157, R.161 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.157 Water bridges: A:K.156, A:S.157 EDO.12: 3 residues within 4Å: Chain A: E.262, A.331, T.332 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.262 Water bridges: A:I.197 EDO.14: 5 residues within 4Å: Chain A: V.28, L.33, K.36, Y.159, E.170 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.36, A:K.36, A:Y.159 Water bridges: A:V.28, A:V.28 EDO.15: 7 residues within 4Å: Chain A: L.35, A.39, E.42, K.156, L.189, D.190, D.191 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.35, A:A.39, A:D.191 EDO.19: 4 residues within 4Å: Chain A: Q.82, S.84, S.85 Ligands: SO4.4 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.85 EDO.20: 4 residues within 4Å: Chain A: T.471, L.472, F.473, S.474 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.162, A:H.218 EDO.26: 2 residues within 4Å: Chain A: V.405, A.432 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.405 EDO.28: 2 residues within 4Å: Chain A: Y.298, H.399 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.399

7 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.13: 3 residues within 4Å: Chain A: Y.182, E.198, T.199 No protein-ligand interaction detected (PLIP) PEG.17: 4 residues within 4Å: Chain A: Y.482, T.488, R.489, F.490 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.489 PEG.21: 2 residues within 4Å: Chain A: A.167, W.168 No protein-ligand interaction detected (PLIP) PEG.22: 9 residues within 4Å: Chain A: G.99, R.100, R.102, V.132, G.134, P.135, V.462, Y.463, G.464 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.462, A:G.464 PEG.23: 9 residues within 4Å: Chain A: V.136, T.137, T.138, G.139, P.140, K.221, A.223, H.465, D.466 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.137, A:H.465 PEG.25: 4 residues within 4Å: Chain A: E.282, E.285, R.319, E.323 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.282, A:E.323 PEG.27: 4 residues within 4Å: Chain A: Y.373, N.403, S.407, H.409 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.403 Water bridges: A:Y.373

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.24: 4 residues within 4Å: Chain A: E.213, R.216, Y.237, F.238 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.237, A:F.238 Water bridges: A:G.240

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.29: 2 residues within 4Å: Chain A: S.474, R.475 Ligand excluded by PLIP CL.30: 2 residues within 4Å: Chain A: R.96, N.97 Ligand excluded by PLIP CL.31: 1 residues within 4Å: Chain A: R.470 Ligand excluded by PLIP

1 x NA: SODIUM ION(Non-functional Binders)

NA.32: 4 residues within 4Å: Chain A: S.279, A.280, A.300, P.301 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.280, A:A.300 Water bridges: A:D.281

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tang, S. et al., Mycobaterium tuberculosis Pks13 acyltransferase incubated with DMSO. To Be Published

Release Date

2025-05-21

Peptides

Polyketide synthase Pks13: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Polyketide synthase Pks13

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