SMTL ID : 8oqn.1

Structure of Mycobacterium tuberculosis beta-oxidation trifunctional enzyme in complex with Fragment-M-53

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-2-2-mer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: H.8, H.9, H.10 Ligand excluded by PLIP SO4.2: 3 residues within 4Å: Chain A: P.647, L.648 Chain D: H.243 Ligand excluded by PLIP SO4.3: 2 residues within 4Å: Chain A: S.674, T.675 Ligand excluded by PLIP SO4.4: 2 residues within 4Å: Chain A: P.236, K.239 Ligand excluded by PLIP SO4.10: 3 residues within 4Å: Chain B: V.290, D.291 Chain D: H.24 Ligand excluded by PLIP SO4.11: 3 residues within 4Å: Chain B: P.647, L.648 Chain C: H.243 Ligand excluded by PLIP SO4.12: 2 residues within 4Å: Chain B: R.614, R.628 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain B: G.709, K.710, A.711 Ligand excluded by PLIP SO4.14: 3 residues within 4Å: Chain B: S.674, T.675, A.676 Ligand excluded by PLIP SO4.15: 2 residues within 4Å: Chain B: P.236, K.239 Ligand excluded by PLIP SO4.16: 2 residues within 4Å: Chain B: H.7, H.8 Ligand excluded by PLIP SO4.23: 1 residues within 4Å: Chain C: R.382 Ligand excluded by PLIP SO4.24: 4 residues within 4Å: Chain C: S.163, R.164, N.249, V.251 Ligand excluded by PLIP SO4.25: 2 residues within 4Å: Chain C: R.195, L.201 Ligand excluded by PLIP SO4.26: 2 residues within 4Å: Chain C: P.193, R.195 Ligand excluded by PLIP SO4.27: 4 residues within 4Å: Chain C: R.173, K.177, D.345, E.346 Ligand excluded by PLIP SO4.28: 3 residues within 4Å: Chain C: N.380, R.382, R.402 Ligand excluded by PLIP SO4.29: 6 residues within 4Å: Chain B: K.267 Chain C: G.232, G.233, F.234, D.235, D.236 Ligand excluded by PLIP SO4.30: 1 residues within 4Å: Chain D: R.402 Ligand excluded by PLIP SO4.31: 2 residues within 4Å: Chain D: R.195, L.201 Ligand excluded by PLIP SO4.32: 2 residues within 4Å: Chain D: P.193, R.195 Ligand excluded by PLIP SO4.33: 3 residues within 4Å: Chain D: S.163, R.164, N.249 Ligand excluded by PLIP SO4.34: 5 residues within 4Å: Chain D: R.42, H.43, P.44, D.45, L.46 Ligand excluded by PLIP SO4.35: 1 residues within 4Å: Chain D: R.382 Ligand excluded by PLIP

11 x W3U: 1-benzyl-1H-pyrazole-4-carboxylic acid(Non-covalent)

W3U.5: 9 residues within 4Å: Chain A: P.273, M.274, P.275, R.278, S.305, G.309, Q.310, V.311 Chain D: Y.142 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:P.275, A:P.275, D:Y.142 Hydrogen bonds: A:Q.310, A:V.311 Water bridges: A:G.309, A:A.312 W3U.6: 12 residues within 4Å: Chain A: M.46, G.84, M.89, V.104, I.107, E.135, E.157, L.163, P.164, G.165, G.166, F.303 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.104, A:F.303 Hydrogen bonds: A:E.157, A:G.165, A:G.166 Water bridges: A:G.132, A:E.157 W3U.7: 10 residues within 4Å: Chain A: Q.179, F.182, V.183, I.257, S.260, F.261, N.264 Chain D: L.231, G.232 Ligands: W3U.9 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:F.182, A:F.182, A:V.183, A:F.261, A:N.264 Hydrogen bonds: A:S.260, A:N.264, D:G.232 pi-Stacking: A:F.261 W3U.8: 5 residues within 4Å: Chain A: S.528, G.532, N.536, L.575, I.579 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.575, A:I.579 Hydrogen bonds: A:N.536, A:N.536 W3U.9: 8 residues within 4Å: Chain A: V.183, A.187, Q.188, N.264, Q.268, L.269, M.274 Ligands: W3U.7 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.183, A:Q.188, A:Q.268 W3U.17: 6 residues within 4Å: Chain B: A.187, Q.188, Q.268, L.269, M.274 Ligands: W3U.18 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Q.268 W3U.18: 9 residues within 4Å: Chain B: Q.179, F.182, V.183, I.257, S.260, F.261, N.264 Chain C: L.231 Ligands: W3U.17 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:F.182, B:F.182, B:V.183, B:F.261, B:N.264 Hydrogen bonds: B:S.260, B:N.264 pi-Stacking: B:F.261, B:F.261 W3U.19: 9 residues within 4Å: Chain B: P.273, M.274, P.275, R.278, S.305, G.309, Q.310, V.311 Chain C: Y.142 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:P.273, B:P.275, B:P.275, C:Y.142 Hydrogen bonds: B:Q.310, B:V.311 W3U.20: 12 residues within 4Å: Chain B: M.46, M.89, V.100, T.103, V.104, I.107, E.135, E.157, P.164, G.165, G.166, F.303 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.100, B:T.103, B:V.104, B:F.303 Hydrogen bonds: B:G.165, B:G.166 W3U.21: 5 residues within 4Å: Chain B: F.176, N.180, S.184, K.196, I.200 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.176, B:N.180 Salt bridges: B:K.196 pi-Stacking: B:F.176 W3U.22: 5 residues within 4Å: Chain B: S.528, G.532, N.536, M.576, I.579 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.579 Hydrogen bonds: B:N.536, B:N.536

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dalwani, S. et al., Crystallographic fragment-binding studies of the Mycobacterium tuberculosis trifunctional enzyme suggest binding pockets for the tails of the acyl-CoA substrates at its active sites and a potential substrate-channeling path between them. Acta Crystallogr D Struct Biol (2024)

Release Date

2024-01-24

Peptides

3-hydroxyacyl-CoA dehydrogenase: AB
Putative acyltransferase Rv0859: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

3-hydroxyacyl-CoA dehydrogenase

Putative acyltransferase Rv0859

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