SMTL ID : 8oqs.1

Structure of Mycobacterium tuberculosis beta-oxidation trifunctional enzyme in complex with Fragment-M-83

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.33 Å

Oligo State

hetero-2-2-mer

Ligands

29 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: 3 residues within 4Å: Chain A: V.290, D.291 Chain C: H.24 Ligand excluded by PLIP SO4.3: 5 residues within 4Å: Chain A: H.7, H.8, H.9, H.10, Q.12 Ligand excluded by PLIP SO4.4: 3 residues within 4Å: Chain A: R.614, K.627, R.628 Ligand excluded by PLIP SO4.5: 3 residues within 4Å: Chain A: P.647, L.648 Chain D: H.243 Ligand excluded by PLIP SO4.6: 1 residues within 4Å: Chain A: R.343 Ligand excluded by PLIP SO4.7: 4 residues within 4Å: Chain A: T.673, S.674, T.675, A.676 Ligand excluded by PLIP SO4.15: 4 residues within 4Å: Chain B: P.275, G.309, Q.310, V.311 Ligand excluded by PLIP SO4.16: 4 residues within 4Å: Chain B: Q.289, V.290, D.291 Chain D: H.24 Ligand excluded by PLIP SO4.17: 3 residues within 4Å: Chain B: P.647, L.648 Chain C: H.243 Ligand excluded by PLIP SO4.18: 2 residues within 4Å: Chain B: R.343, K.419 Ligand excluded by PLIP SO4.19: 3 residues within 4Å: Chain B: R.614, K.627, R.628 Ligand excluded by PLIP SO4.20: 3 residues within 4Å: Chain B: G.709, K.710, A.711 Ligand excluded by PLIP SO4.21: 3 residues within 4Å: Chain B: T.673, S.674, T.675 Ligand excluded by PLIP SO4.22: 2 residues within 4Å: Chain B: P.236, K.239 Ligand excluded by PLIP SO4.24: 4 residues within 4Å: Chain B: H.8, H.9, H.10, Q.12 Ligand excluded by PLIP SO4.30: 1 residues within 4Å: Chain C: R.382 Ligand excluded by PLIP SO4.31: 4 residues within 4Å: Chain C: S.163, R.164, N.249, V.251 Ligand excluded by PLIP SO4.32: 2 residues within 4Å: Chain C: R.195, L.201 Ligand excluded by PLIP SO4.33: 2 residues within 4Å: Chain C: P.193, R.195 Ligand excluded by PLIP SO4.34: 5 residues within 4Å: Chain C: R.42, H.43, P.44, D.45, L.46 Ligand excluded by PLIP SO4.35: 3 residues within 4Å: Chain C: N.380, R.382, R.402 Ligand excluded by PLIP SO4.36: 6 residues within 4Å: Chain B: K.267 Chain C: G.232, G.233, F.234, D.235, D.236 Ligand excluded by PLIP SO4.38: 2 residues within 4Å: Chain D: R.382, R.402 Ligand excluded by PLIP SO4.39: 2 residues within 4Å: Chain D: R.195, L.201 Ligand excluded by PLIP SO4.40: 2 residues within 4Å: Chain D: P.193, R.195 Ligand excluded by PLIP SO4.41: 4 residues within 4Å: Chain D: S.163, R.164, N.249, V.251 Ligand excluded by PLIP SO4.42: 4 residues within 4Å: Chain D: H.43, P.44, D.45, L.46 Ligand excluded by PLIP SO4.43: 1 residues within 4Å: Chain D: R.382 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 3 residues within 4Å: Chain A: G.725, D.726, R.727 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.726, A:R.727, A:R.727 GOL.23: 2 residues within 4Å: Chain B: D.27, A.28 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.28

13 x VWZ: 4-phenylbenzenesulfonic acid(Non-covalent)

VWZ.9: 10 residues within 4Å: Chain A: T.458, P.460, R.523, G.524, S.528, R.529, I.579, A.582, T.583 Ligands: VWZ.13 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:R.523, A:I.579, A:I.579, A:A.582 VWZ.10: 7 residues within 4Å: Chain A: M.486, P.487, P.561, I.683, M.684, I.686, G.687 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.487, A:P.561 VWZ.11: 11 residues within 4Å: Chain A: T.88, M.89, Q.91, A.92, D.96, D.99, V.100, T.103, F.303, V.307 Ligands: VWZ.12 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:T.88, A:M.89, A:A.92, A:D.99, A:V.100, A:T.103, A:F.303, A:V.307 VWZ.12: 16 residues within 4Å: Chain A: M.46, I.51, G.84, D.85, T.88, M.89, T.103, I.107, G.132, E.135, E.157, L.163, G.165, G.166, F.303 Ligands: VWZ.11 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.51, A:D.85, A:T.88, A:T.103, A:I.107 Hydrogen bonds: A:G.132, A:E.135, A:G.165, A:G.166 VWZ.13: 11 residues within 4Å: Chain A: S.457, H.478, S.528, I.531, G.532, N.536, L.571, L.575, M.576, I.579 Ligands: VWZ.9 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.531, A:L.575, A:M.576, A:I.579, A:I.579 Hydrogen bonds: A:S.457, A:S.528 VWZ.14: 8 residues within 4Å: Chain A: H.8, S.11, Q.12, D.13, S.16, M.17, P.18, E.48 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Q.12, A:Q.12, A:P.18, A:E.48 Hydrogen bonds: A:Q.12 pi-Stacking: A:H.8 VWZ.25: 7 residues within 4Å: Chain B: M.486, P.487, P.561, I.683, M.684, I.686, G.687 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:P.487, B:P.561 VWZ.26: 10 residues within 4Å: Chain B: T.88, M.89, A.92, D.96, D.99, V.100, T.103, F.303, V.307 Ligands: VWZ.27 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:T.88, B:A.92, B:D.99, B:V.100, B:V.100, B:T.103, B:F.303, B:V.307 Hydrogen bonds: B:D.99 VWZ.27: 18 residues within 4Å: Chain B: M.46, E.48, I.51, G.84, D.85, T.88, M.89, T.103, V.104, I.107, G.132, E.135, E.157, L.163, G.165, G.166, F.303 Ligands: VWZ.26 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.51, B:D.85, B:T.88, B:T.103, B:V.104, B:I.107 Hydrogen bonds: B:G.132, B:G.165, B:G.166 VWZ.28: 7 residues within 4Å: Chain B: S.457, S.528, N.536, L.571, L.575, M.576, I.579 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.571, B:M.576, B:I.579, B:I.579 Hydrogen bonds: B:S.457 VWZ.29: 9 residues within 4Å: Chain B: H.8, S.11, Q.12, D.13, S.16, M.17, P.18, E.48, E.52 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Q.12, B:Q.12, B:P.18, B:E.48 Hydrogen bonds: B:Q.12 pi-Cation interactions: B:H.8 VWZ.37: 13 residues within 4Å: Chain C: F.91, M.127, M.134, V.144, M.145, F.146, V.147, Q.149, P.296, M.299, G.391, G.392 Chain D: L.75 9 PLIP interactions: 1 interactions with chain D, 8 interactions with chain C Hydrophobic interactions: D:L.75, C:V.144, C:F.146, C:F.146, C:Q.149, C:P.296 Hydrogen bonds: C:Q.149, C:G.391 pi-Stacking: C:F.91 VWZ.44: 13 residues within 4Å: Chain C: L.75 Chain D: F.91, M.127, M.134, V.144, M.145, F.146, V.147, Q.149, P.296, M.299, G.391, G.392 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:V.144, D:F.146, D:F.146, C:L.75 Hydrogen bonds: D:Q.149, D:G.391 pi-Stacking: D:F.91

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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