SMTL ID : 8oqu.1

Structure of Mycobacterium tuberculosis beta-oxidation trifunctional enzyme in complex with Fragment-M-92

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.89 Å

Oligo State

hetero-2-2-mer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: P.275, G.309, Q.310, V.311 Ligand excluded by PLIP SO4.2: 4 residues within 4Å: Chain A: H.7, H.8, H.9, H.10 Ligand excluded by PLIP SO4.3: 4 residues within 4Å: Chain A: R.614, G.626, K.627, R.628 Ligand excluded by PLIP SO4.4: 3 residues within 4Å: Chain A: P.647, L.648 Chain D: H.243 Ligand excluded by PLIP SO4.5: 3 residues within 4Å: Chain A: S.674, T.675, A.676 Ligand excluded by PLIP SO4.12: 3 residues within 4Å: Chain B: G.309, Q.310, V.311 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain B: V.290, D.291 Chain D: H.24 Ligand excluded by PLIP SO4.14: 4 residues within 4Å: Chain B: P.646, P.647, L.648 Chain C: H.243 Ligand excluded by PLIP SO4.15: 3 residues within 4Å: Chain B: S.674, T.675, A.676 Ligand excluded by PLIP SO4.21: 4 residues within 4Å: Chain A: Q.289, V.290, D.291 Chain C: H.24 Ligand excluded by PLIP SO4.22: 1 residues within 4Å: Chain C: R.382 Ligand excluded by PLIP SO4.23: 3 residues within 4Å: Chain C: S.163, R.164, N.249 Ligand excluded by PLIP SO4.24: 2 residues within 4Å: Chain C: R.195, L.201 Ligand excluded by PLIP SO4.25: 2 residues within 4Å: Chain C: P.193, R.195 Ligand excluded by PLIP SO4.26: 4 residues within 4Å: Chain C: R.173, K.177, D.345, E.346 Ligand excluded by PLIP SO4.27: 3 residues within 4Å: Chain C: N.380, R.382, R.402 Ligand excluded by PLIP SO4.28: 2 residues within 4Å: Chain D: N.380, R.402 Ligand excluded by PLIP SO4.29: 2 residues within 4Å: Chain D: R.195, L.201 Ligand excluded by PLIP SO4.30: 2 residues within 4Å: Chain D: P.193, R.195 Ligand excluded by PLIP SO4.31: 4 residues within 4Å: Chain D: S.163, R.164, N.249, V.251 Ligand excluded by PLIP SO4.32: 2 residues within 4Å: Chain D: R.382, R.402 Ligand excluded by PLIP

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 3 residues within 4Å: Chain A: G.725, D.726, R.727 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.726, A:R.727 GOL.7: 5 residues within 4Å: Chain A: S.457, S.528, L.571, L.575, I.579 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.457, A:S.457 GOL.8: 10 residues within 4Å: Chain A: M.46, E.135, E.157, L.163, P.164, G.165, G.166, F.303 Ligands: VXN.9, VXN.11 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.163, A:G.165, A:G.166 GOL.16: 5 residues within 4Å: Chain B: S.457, S.528, L.571, L.575, I.579 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.457, B:S.528 GOL.17: 9 residues within 4Å: Chain B: M.46, E.135, E.157, P.164, G.165, G.166, F.303 Ligands: VXN.19, VXN.20 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.135, B:E.157, B:G.165, B:G.166

6 x VXN: 4-chloranylbenzenesulfonic acid(Non-covalent)

VXN.9: 9 residues within 4Å: Chain A: H.7, M.46, N.47, E.48, I.51, D.85, M.89 Ligands: GOL.8, VXN.10 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.51 Hydrogen bonds: A:T.103 Salt bridges: A:H.7 VXN.10: 7 residues within 4Å: Chain A: T.88, M.89, D.96, D.99, V.100, T.103 Ligands: VXN.9 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.100 VXN.11: 11 residues within 4Å: Chain A: G.83, G.84, D.85, V.86, M.89, L.130, G.131, P.156, E.157, L.160 Ligands: GOL.8 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.86, A:E.157, A:L.160 Hydrogen bonds: A:G.83 VXN.18: 8 residues within 4Å: Chain B: T.88, M.89, A.92, D.96, D.99, V.100, T.103 Ligands: VXN.19 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:T.88, B:A.92, B:V.100, B:V.100 Hydrogen bonds: B:D.96, B:D.99 VXN.19: 10 residues within 4Å: Chain B: H.7, M.46, N.47, E.48, D.85, T.88, M.89, T.103 Ligands: GOL.17, VXN.18 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:E.48, B:T.88 Salt bridges: B:H.7 VXN.20: 10 residues within 4Å: Chain B: G.83, G.84, V.86, M.89, L.130, G.131, P.156, E.157, L.160 Ligands: GOL.17 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.86, B:E.157, B:L.160 Hydrogen bonds: B:G.132

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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