SMTL ID : 9c1d.2 (1 other biounit)

Mycobaterium tuberculosis Pks13 acyltransferase incubated with DMSO

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 9 residues within 4Å: Chain A: F.147, Q.201, S.229, L.230, R.254, M.258, S.336, H.337 Ligands: P33.5 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.201, A:L.230, A:S.336 Water bridges: A:S.229, A:S.229 Salt bridges: A:R.254, A:H.337 SO4.2: 2 residues within 4Å: Chain A: N.418, R.445 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.418, A:N.418 Salt bridges: A:R.445 SO4.3: 4 residues within 4Å: Chain A: A.59, F.60, R.64, R.489 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:F.60 Water bridges: A:S.58, A:R.64, A:T.488 Salt bridges: A:R.64, A:R.489 SO4.4: 3 residues within 4Å: Chain A: R.96, N.97, R.489 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.97 Water bridges: A:R.489 Salt bridges: A:R.489 SO4.25: 3 residues within 4Å: Chain A: Q.447 Chain B: D.6, E.7 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:E.7, A:Q.447, A:Q.447

1 x P33: 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL(Non-covalent)

P33.5: 18 residues within 4Å: Chain A: Q.150, Y.195, I.197, T.200, Q.201, M.258, G.261, E.262, L.265, M.273, A.331, T.332, G.334, S.336, Q.340, M.341, L.344 Ligands: SO4.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.150, A:Y.195, A:Q.201, A:T.332 Water bridges: A:A.331, A:A.331

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

EDO.6: 6 residues within 4Å: Chain A: P.51, L.52, V.450, V.454 Ligands: EDO.12, EDO.17 1 PLIP interactions: 1 interactions with chain A Water bridges: A:L.52 EDO.8: 3 residues within 4Å: Chain A: Q.125, V.129, F.130 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.125, A:Q.125 Water bridges: A:A.126 EDO.12: 3 residues within 4Å: Chain A: R.161, V.450 Ligands: EDO.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.161 EDO.16: 7 residues within 4Å: Chain A: S.84, S.85, S.88, Q.480, Y.482, A.483, N.484 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.85, A:S.88 Water bridges: A:N.484, A:N.484 EDO.17: 5 residues within 4Å: Chain A: T.471, L.472, F.473, S.474 Ligands: EDO.6 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.474 EDO.18: 6 residues within 4Å: Chain A: V.136, T.137, T.138, G.139, P.140, H.465 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.136 Water bridges: A:D.466 EDO.19: 2 residues within 4Å: Chain A: A.167, W.168 No protein-ligand interaction detected (PLIP) EDO.21: 3 residues within 4Å: Chain A: T.29, E.30, E.31 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.29, A:E.30, A:E.31 Water bridges: A:E.186

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

DMS.7: 3 residues within 4Å: Chain A: G.123, K.124, Q.125 No protein-ligand interaction detected (PLIP) DMS.9: 1 residues within 4Å: Chain A: R.445 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.445 DMS.10: 5 residues within 4Å: Chain A: H.151, R.152, K.153, R.445 Ligands: CL.22 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.151, A:R.152, A:K.153 DMS.13: 4 residues within 4Å: Chain A: R.284, L.293, E.294, V.295 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.284, A:V.295 DMS.14: 2 residues within 4Å: Chain A: H.399, R.402 No protein-ligand interaction detected (PLIP)

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

PEG.11: 3 residues within 4Å: Chain A: Y.182, E.198, T.199 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.198, A:E.198 PEG.15: 3 residues within 4Å: Chain A: V.405, G.433, L.434 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.433 Water bridges: A:G.408 PEG.20: 3 residues within 4Å: Chain A: L.86, D.109, H.110 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.86, A:H.110, A:H.110, A:D.111 Water bridges: A:E.87

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

CL.22: 3 residues within 4Å: Chain A: H.151, R.152 Ligands: DMS.10 Ligand excluded by PLIP CL.23: 1 residues within 4Å: Chain A: R.392 Ligand excluded by PLIP CL.24: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

Polyketide synthase Pks13

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