SMTL ID : 5w2o.1

Crystal structure of Mycobacterium tuberculosis KasA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

NA.1: 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.332, A:N.423 NA.11: 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:N.332, B:E.377, B:N.423

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: A.41, V.42, E.53, S.120, L.285, R.386 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.42, A:V.42, A:E.53, A:R.386 GOL.3: 3 residues within 4Å: Chain A: L.60, D.387, Y.414 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.414, A:Y.414 GOL.4: 12 residues within 4Å: Chain A: E.222, G.223, P.224, I.225, E.226, P.229, F.262, G.263, E.264, H.368, S.369, I.370 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.224, A:E.226, A:G.263, A:S.369 GOL.5: 4 residues within 4Å: Chain A: F.298, A.304, A.305, D.306 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.305, A:D.306, A:D.306 GOL.12: 6 residues within 4Å: Chain B: A.41, V.42, E.53, S.120, L.285, R.386 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:V.42, B:V.42, B:E.53, B:E.53, B:R.386 GOL.13: 3 residues within 4Å: Chain B: L.60, D.387, Y.414 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.414 Water bridges: B:Y.414 GOL.14: 12 residues within 4Å: Chain B: E.222, G.223, P.224, I.225, E.226, P.229, F.262, G.263, E.264, H.368, S.369, I.370 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:P.224, B:E.226, B:G.263, B:S.369 GOL.15: 4 residues within 4Å: Chain B: F.298, A.304, A.305, D.306 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.305, B:D.306, B:D.306

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

IPA.6: 3 residues within 4Å: Chain A: M.236, T.338, I.340 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.338, A:I.340 IPA.7: 3 residues within 4Å: Chain A: N.347, R.350, V.351 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:R.350 Hydrogen bonds: A:V.351 IPA.8: 7 residues within 4Å: Chain A: Q.166, M.169, N.171, G.172 Chain B: A.193, M.300, F.427 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.171, B:F.427 IPA.16: 3 residues within 4Å: Chain B: M.236, T.338, I.340 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:T.338, B:I.340 IPA.17: 3 residues within 4Å: Chain B: N.347, R.350, V.351 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:R.350 Hydrogen bonds: B:V.351 IPA.18: 7 residues within 4Å: Chain A: A.193, M.300, F.427 Chain B: Q.166, M.169, N.171, G.172 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:F.427, B:N.171

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

TCE.9: 8 residues within 4Å: Chain A: W.118, P.124, E.125, V.126, L.179, Q.180, L.181, G.182 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:P.124, A:V.126, A:Q.180 Water bridges: A:Q.180, A:Q.180, A:R.184 TCE.19: 8 residues within 4Å: Chain B: W.118, P.124, E.125, V.126, L.179, Q.180, L.181, G.182 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:P.124, B:V.126, B:Q.180 Water bridges: B:Q.180, B:Q.180, B:R.184

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

CL.10: 3 residues within 4Å: Chain A: V.408, A.409, R.413 Ligand excluded by PLIP CL.20: 3 residues within 4Å: Chain B: V.408, A.409, R.413 Ligand excluded by PLIP

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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