SMTL ID : 6p9m.1

Crystal structure of Mycobacterium tuberculosis KasA in complex with O6J

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.26 Å

Oligo State

homo-dimer

Ligands

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

NA.1: 6 residues within 4Å: Chain A: N.307, A.308, H.309, E.352, N.397, N.398 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.398, A:N.398 NA.8: 6 residues within 4Å: Chain B: N.307, A.308, H.309, E.352, N.397, N.398 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.307, B:N.398

2 x O6J: N-(2-cyano-3-methyl-1H-indol-5-yl)pentane-1-sulfonamide(Non-covalent)

O6J.2: 16 residues within 4Å: Chain A: L.114, G.115, E.118, E.197, G.198, P.199, I.200, E.201, P.204, F.237, G.238, E.239, H.343, S.344, I.345 Ligands: IPA.7 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.114, A:I.200, A:E.201, A:F.237, A:F.237, A:E.239, A:I.345 Hydrogen bonds: A:E.118 Water bridges: A:Y.80 O6J.9: 16 residues within 4Å: Chain B: L.114, G.115, E.118, E.197, G.198, P.199, I.200, E.201, P.204, F.237, G.238, E.239, H.343, S.344, I.345 Ligands: IPA.14 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.114, B:I.200, B:E.201, B:F.237, B:F.237, B:E.239, B:I.345 Hydrogen bonds: B:E.118 Water bridges: B:Y.80

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: A.16, V.17, I.27, E.28, S.95 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.17, A:V.17, A:S.95 GOL.4: 4 residues within 4Å: Chain A: F.273, A.279, A.280, D.281 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.280, A:D.281 Water bridges: A:D.281 GOL.10: 5 residues within 4Å: Chain B: A.16, V.17, I.27, E.28, S.95 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.17, B:V.17, B:E.28, B:S.95 GOL.11: 4 residues within 4Å: Chain B: F.273, A.279, A.280, D.281 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.280, B:D.281 Water bridges: B:D.281

6 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.5: 7 residues within 4Å: Chain A: M.211, A.213, V.276, A.277, T.313, I.315, F.402 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.315, A:F.402 Hydrogen bonds: A:M.211 IPA.6: 3 residues within 4Å: Chain A: N.322, R.325, V.326 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.326 Hydrogen bonds: A:R.325 IPA.7: 6 residues within 4Å: Chain A: G.113, L.114, F.208, I.345 Chain B: M.144 Ligands: O6J.2 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.114, A:I.345, B:M.144 IPA.12: 7 residues within 4Å: Chain B: M.211, A.213, V.276, A.277, T.313, I.315, F.402 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.315, B:F.402 Hydrogen bonds: B:M.211 IPA.13: 3 residues within 4Å: Chain B: N.322, R.325, V.326 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.326 Hydrogen bonds: B:R.325 IPA.14: 6 residues within 4Å: Chain A: M.144 Chain B: G.113, L.114, F.208, I.345 Ligands: O6J.9 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:M.144, B:L.114, B:I.345

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Inoyama, D. et al., A Preclinical Candidate Targeting Mycobacterium tuberculosis KasA. Cell Chem Biol (2020)

Release Date

2020-04-01

Peptides

3-oxoacyl-[acyl-carrier-protein] synthase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

3-oxoacyl-[acyl-carrier-protein] synthase 1

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