SMTL ID : 8oqp.1

Structure of Mycobacterium tuberculosis beta-oxidation trifunctional enzyme in complex with Fragment-M-76

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.18 Å

Oligo State

hetero-2-2-mer

Ligands

19 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: 2 residues within 4Å: Chain A: R.614, R.628 Ligand excluded by PLIP SO4.3: 3 residues within 4Å: Chain A: P.647, L.648 Chain D: H.243 Ligand excluded by PLIP SO4.12: 3 residues within 4Å: Chain A: F.192, K.193, K.196 Ligand excluded by PLIP SO4.13: 4 residues within 4Å: Chain A: Q.289, V.290, D.291 Chain C: H.24 Ligand excluded by PLIP SO4.14: 4 residues within 4Å: Chain B: P.275, G.309, Q.310, V.311 Ligand excluded by PLIP SO4.15: 3 residues within 4Å: Chain B: P.647, L.648 Chain C: H.243 Ligand excluded by PLIP SO4.16: 3 residues within 4Å: Chain B: R.614, G.626, R.628 Ligand excluded by PLIP SO4.23: 3 residues within 4Å: Chain B: F.192, K.193, K.196 Ligand excluded by PLIP SO4.24: 4 residues within 4Å: Chain B: Q.289, V.290, D.291 Chain D: H.24 Ligand excluded by PLIP SO4.25: 1 residues within 4Å: Chain C: R.382 Ligand excluded by PLIP SO4.26: 4 residues within 4Å: Chain C: S.163, R.164, N.249, V.251 Ligand excluded by PLIP SO4.27: 2 residues within 4Å: Chain C: P.193, R.195 Ligand excluded by PLIP SO4.28: 3 residues within 4Å: Chain C: N.380, R.382, R.402 Ligand excluded by PLIP SO4.31: 3 residues within 4Å: Chain C: L.311, T.317, V.318 Ligand excluded by PLIP SO4.32: 2 residues within 4Å: Chain D: N.380, R.402 Ligand excluded by PLIP SO4.33: 2 residues within 4Å: Chain D: P.193, R.195 Ligand excluded by PLIP SO4.34: 4 residues within 4Å: Chain D: S.163, R.164, N.249, V.251 Ligand excluded by PLIP SO4.40: 1 residues within 4Å: Chain D: R.382 Ligand excluded by PLIP

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: G.725, D.726, R.727 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.727 GOL.5: 7 residues within 4Å: Chain A: M.46, M.89, I.107, E.135, E.157, G.166, F.303 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.135 Water bridges: A:G.132 GOL.6: 5 residues within 4Å: Chain A: H.478, F.480, T.527, S.528, L.571 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.527, A:S.528 GOL.17: 7 residues within 4Å: Chain B: S.457, H.478, F.480, S.528, I.531, L.571, I.686 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.457, B:S.528 GOL.18: 6 residues within 4Å: Chain B: V.104, G.132, E.135, E.157, G.166, F.303 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.157, B:E.157 Water bridges: B:D.85, B:D.85, B:G.132 GOL.35: 3 residues within 4Å: Chain D: R.308, T.317, V.318 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:V.318 GOL.36: 1 residues within 4Å: Chain D: H.205 1 PLIP interactions: 1 interactions with chain D Water bridges: D:D.206

14 x VXZ: 2-azanyl-5-sulfo-benzoic acid(Non-covalent)

VXZ.7: 11 residues within 4Å: Chain A: G.83, G.84, L.130, G.131, P.156, E.157, T.159, L.160, R.191, F.319, F.320 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:P.156, A:L.160, A:L.160 Hydrogen bonds: A:G.83, A:G.84, A:F.319 Water bridges: A:G.132 VXZ.8: 4 residues within 4Å: Chain A: N.572, S.612, L.615, K.616 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.615, A:K.616 Hydrogen bonds: A:N.572, A:S.612, A:L.615 Salt bridges: A:K.616 VXZ.9: 2 residues within 4Å: Chain A: A.711, R.718 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.718 VXZ.10: 8 residues within 4Å: Chain A: M.486, I.531, P.561, L.567, I.683, M.684, I.686, G.687 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.561, A:P.561 Hydrogen bonds: A:I.686 Water bridges: A:A.562 VXZ.11: 5 residues within 4Å: Chain A: Q.664, L.667, T.673, S.674, T.675 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:T.675 Hydrogen bonds: A:Q.664, A:L.667, A:T.675, A:T.675 Water bridges: A:A.676 VXZ.19: 5 residues within 4Å: Chain B: N.572, E.574, S.612, L.615, K.616 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.615, B:K.616 Hydrogen bonds: B:N.572, B:S.612, B:L.615 Salt bridges: B:K.616 VXZ.20: 11 residues within 4Å: Chain B: G.83, L.130, G.131, P.156, E.157, T.159, L.160, R.191, F.319, F.320, Q.324 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:P.156, B:L.160 Hydrogen bonds: B:G.84, B:R.191, B:Q.324 Water bridges: B:G.132, B:E.157, B:F.319 VXZ.21: 6 residues within 4Å: Chain B: S.643, S.644, Q.645, P.646, P.647, Y.724 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:P.646 Hydrogen bonds: B:Q.645, B:Y.724, B:Y.724 VXZ.22: 5 residues within 4Å: Chain B: Q.664, L.667, T.673, S.674, T.675 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:T.675 Hydrogen bonds: B:Q.664, B:L.667, B:T.675, B:T.675 VXZ.29: 7 residues within 4Å: Chain C: Y.8, E.9, R.42, K.189, T.281, R.283, D.374 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:R.283 Hydrogen bonds: C:Y.8, C:D.374 Water bridges: C:R.42, C:R.283 Salt bridges: C:K.189, C:R.283 pi-Cation interactions: C:R.283 VXZ.30: 2 residues within 4Å: Chain C: R.378, R.379 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:R.379 Hydrogen bonds: C:R.378, C:R.378 Salt bridges: C:R.378, C:R.379, C:R.379 VXZ.37: 7 residues within 4Å: Chain D: E.9, R.42, K.189, T.281, R.283, D.374, E.377 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:R.283 Hydrogen bonds: D:Y.8 Water bridges: D:R.42, D:R.283 Salt bridges: D:K.189, D:R.283 pi-Cation interactions: D:R.283 VXZ.38: 7 residues within 4Å: Chain D: L.46, D.47, E.48, N.49, G.78, M.79, P.80 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:E.48, D:P.80, D:P.80 Hydrogen bonds: D:D.47, D:E.48, D:N.49, D:N.49, D:N.49, D:G.78 Water bridges: D:V.81 VXZ.39: 2 residues within 4Å: Chain D: R.378, R.379 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:R.379 Hydrogen bonds: D:R.378, D:R.378 Salt bridges: D:R.378, D:R.379, D:R.379

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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