SMTL ID : 5w2q.1

Crystal structure of Mycobacterium tuberculosis KasA in complex with 6U5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

4 x 6U5: ~{N}-(1-methylindazol-6-yl)butane-1-sulfonamide(Non-covalent)

6U5.1: 13 residues within 4Å: Chain A: G.140, E.143, E.222, G.223, P.224, I.225, E.226, P.229, F.262, E.264, H.368, I.370 Ligands: 6U5.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.225, A:F.262, A:F.262, A:E.264 Hydrogen bonds: A:E.222, A:G.223 6U5.2: 14 residues within 4Å: Chain A: G.138, L.139, A.142, E.222, L.228, P.229, A.232, F.233, I.370 Chain B: I.145, V.165, I.168, M.169 Ligands: 6U5.1 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:I.145, B:V.165, B:I.168, A:L.139, A:A.142 pi-Stacking: A:F.233 6U5.9: 13 residues within 4Å: Chain B: G.140, E.143, E.222, G.223, P.224, I.225, E.226, P.229, F.262, E.264, H.368, I.370 Ligands: 6U5.10 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.225, B:F.262, B:F.262, B:E.264 Hydrogen bonds: B:E.222, B:E.222, B:G.223 6U5.10: 14 residues within 4Å: Chain A: I.145, V.165, I.168, M.169 Chain B: G.138, L.139, A.142, E.222, L.228, P.229, A.232, F.233, I.370 Ligands: 6U5.9 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:I.145, A:V.165, A:I.168, B:L.139, B:A.142 pi-Stacking: B:F.233

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: A.41, V.42, I.52, E.53 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.42, A:V.42, A:R.386 Water bridges: A:E.53, A:S.120 GOL.11: 4 residues within 4Å: Chain B: A.41, V.42, I.52, E.53 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:V.42, B:V.42, B:E.53, B:R.386 Water bridges: B:E.53, B:S.120

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

NA.4: 6 residues within 4Å: Chain A: N.332, A.333, H.334, E.377, N.422, N.423 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.423, A:N.423 NA.12: 6 residues within 4Å: Chain B: N.332, A.333, H.334, E.377, N.422, N.423 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.377, B:N.423, B:N.423

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

IPA.5: 6 residues within 4Å: Chain A: V.301, A.302, P.303, I.340, F.427 Ligands: IPA.6 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.301, A:I.340, A:F.427 Water bridges: A:T.338, A:T.338 IPA.6: 4 residues within 4Å: Chain A: R.237, P.339, I.340 Ligands: IPA.5 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.339, A:I.340 IPA.7: 5 residues within 4Å: Chain A: R.102, M.103, V.176, L.179 Chain B: M.300 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.176, A:L.179 IPA.13: 6 residues within 4Å: Chain B: V.301, A.302, P.303, I.340, F.427 Ligands: IPA.14 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.301, B:I.340, B:F.427 Water bridges: B:T.338 IPA.14: 4 residues within 4Å: Chain B: R.237, P.339, I.340 Ligands: IPA.13 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:P.339, B:I.340 IPA.15: 5 residues within 4Å: Chain A: M.300 Chain B: R.102, M.103, V.176, L.179 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.176, B:L.179

2 x TCE: 3,3',3''-phosphanetriyltripropanoic acid(Non-covalent)

TCE.8: 8 residues within 4Å: Chain A: W.118, P.124, E.125, V.126, L.179, Q.180, L.181, G.182 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:P.124, A:V.126, A:Q.180 Water bridges: A:R.184, A:R.184 TCE.16: 8 residues within 4Å: Chain B: W.118, P.124, E.125, V.126, L.179, Q.180, L.181, G.182 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:P.124, B:V.126, B:Q.180 Water bridges: B:R.184, B:R.184

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kumar, P. et al., Synergistic Lethality of a Binary Inhibitor of Mycobacterium tuberculosis KasA. MBio (2018)

Release Date

2018-12-05

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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