SMTL ID : 7o4t.1

Structure of Mycobacterium tuberculosis beta-oxidation trifunctional enzyme with Coenzyme A bound at the hydratase, thiolase active sites and possible additional binding site (CoA(ECH/HAD))

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-2-2-mer

Ligands

6 x COA: COENZYME A(Non-covalent)

COA.1: 17 residues within 4Å: Chain A: S.42, T.43, V.45, A.82, G.83, G.84, D.85, V.86, L.130, G.131, G.132, P.156, E.157, L.160, R.191, F.320, Q.324 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.130 Hydrogen bonds: A:A.82, A:G.84, A:V.86, A:R.191, A:R.191 pi-Stacking: A:F.320, A:F.320 COA.2: 16 residues within 4Å: Chain A: V.158, T.159, A.187, Q.188, L.265, Q.268, L.269, M.274, P.277, M.315, F.319, K.485, P.487, I.683, M.684, P.690 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.159, A:P.277, A:P.690 Hydrogen bonds: A:A.187 COA.12: 18 residues within 4Å: Chain B: S.42, T.43, V.45, A.82, G.83, G.84, D.85, V.86, K.87, L.130, G.131, G.132, P.156, E.157, L.160, R.191, F.320, Q.324 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:A.82, B:L.130 Hydrogen bonds: B:A.82, B:G.84, B:V.86, B:K.87, B:R.191, B:Q.324 Salt bridges: B:K.87 pi-Stacking: B:F.320, B:F.320 COA.14: 13 residues within 4Å: Chain B: V.158, A.187, Q.188, L.269, M.274, P.277, M.315, R.396, K.485, P.561, I.683, M.684, P.690 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.269, B:P.277, B:P.690 Hydrogen bonds: B:Q.188, B:R.396 COA.24: 18 residues within 4Å: Chain C: C.92, M.127, Q.149, Q.175, R.210, T.213, L.218, L.221, A.224, F.225, T.253, G.254, G.255, S.257, S.258, I.260, A.329, H.359 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:F.225, C:F.225 Hydrogen bonds: C:K.19, C:Q.149, C:Q.175, C:R.210, C:R.210, C:T.213, C:S.258 pi-Cation interactions: C:R.210 COA.32: 19 residues within 4Å: Chain D: K.19, C.92, M.127, Q.149, Q.175, R.210, T.213, L.218, L.221, A.224, F.225, T.253, G.254, G.255, S.257, S.258, A.329, F.330, H.359 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:F.225, D:F.225, D:F.330 Hydrogen bonds: D:Q.175, D:R.210, D:R.210, D:T.213, D:T.213, D:S.258 Water bridges: D:I.260 Salt bridges: D:K.19, D:K.19 pi-Cation interactions: D:R.210, D:R.210

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 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.4: 2 residues within 4Å: Chain A: P.245, G.246 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.246 GOL.13: 2 residues within 4Å: Chain B: D.27, A.28 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.28

2 x PAP: 3'-PHOSPHATE-ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

PAP.5: 4 residues within 4Å: Chain A: Q.645 Chain D: H.243, W.244 Ligands: SO4.9 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:H.243, A:Q.645 pi-Stacking: D:W.244, D:W.244, D:W.244 PAP.15: 5 residues within 4Å: Chain B: Q.645 Chain C: I.159, H.243, W.244 Ligands: SO4.17 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:Q.645 Water bridges: B:S.550 pi-Stacking: C:W.244, C:W.244, C:W.244, C:W.244

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

SO4.6: 4 residues within 4Å: Chain A: P.275, G.309, Q.310, V.311 Ligand excluded by PLIP SO4.7: 3 residues within 4Å: Chain A: V.290, D.291 Chain C: H.24 Ligand excluded by PLIP SO4.8: 4 residues within 4Å: Chain A: H.7, H.8, H.9, H.10 Ligand excluded by PLIP SO4.9: 4 residues within 4Å: Chain A: P.647, L.648 Chain D: H.243 Ligands: PAP.5 Ligand excluded by PLIP SO4.10: 4 residues within 4Å: Chain A: T.673, S.674, T.675, A.676 Ligand excluded by PLIP SO4.11: 2 residues within 4Å: Chain A: P.460, R.523 Ligand excluded by PLIP SO4.16: 4 residues within 4Å: Chain B: P.275, G.309, Q.310, V.311 Ligand excluded by PLIP SO4.17: 4 residues within 4Å: Chain B: P.647, L.648 Chain C: H.243 Ligands: PAP.15 Ligand excluded by PLIP SO4.18: 3 residues within 4Å: Chain B: V.290, D.291 Chain D: H.24 Ligand excluded by PLIP SO4.19: 4 residues within 4Å: Chain B: T.708, G.709, K.710, A.711 Ligand excluded by PLIP SO4.20: 3 residues within 4Å: Chain B: H.8, H.9, H.10 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 SO4.23: 3 residues within 4Å: Chain B: P.460, R.523, G.586 Ligand excluded by PLIP SO4.25: 4 residues within 4Å: Chain C: S.163, R.164, N.249, V.251 Ligand excluded by PLIP SO4.26: 3 residues within 4Å: Chain C: N.380, R.382, R.402 Ligand excluded by PLIP SO4.27: 2 residues within 4Å: Chain C: R.195, L.201 Ligand excluded by PLIP SO4.28: 2 residues within 4Å: Chain C: P.193, R.195 Ligand excluded by PLIP SO4.29: 2 residues within 4Å: Chain C: T.317, V.318 Ligand excluded by PLIP SO4.30: 1 residues within 4Å: Chain C: R.382 Ligand excluded by PLIP SO4.31: 2 residues within 4Å: Chain C: Y.186, R.378 Ligand excluded by PLIP SO4.33: 4 residues within 4Å: Chain D: S.163, R.164, N.249, V.251 Ligand excluded by PLIP SO4.34: 1 residues within 4Å: Chain D: R.382 Ligand excluded by PLIP SO4.35: 3 residues within 4Å: Chain D: N.380, R.382, R.402 Ligand excluded by PLIP SO4.36: 2 residues within 4Å: Chain D: R.195, L.201 Ligand excluded by PLIP SO4.37: 2 residues within 4Å: Chain D: P.193, R.195 Ligand excluded by PLIP SO4.38: 2 residues within 4Å: Chain D: Y.186, R.378 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dalwani, S. et al., Substrate specificity and conformational flexibility properties of the Mycobacterium tuberculosis beta-oxidation trifunctional enzyme. J.Struct.Biol. (2021)

Release Date

2021-08-25

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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