SMTL ID : 7o4s.1

Structure of Mycobacterium tuberculosis beta-oxidation trifunctional enzyme with Coenzyme A bound at the hydratase, thiolase active sites and additional binding site (CoA(ECH2))

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.79 Å

Oligo State

hetero-2-2-mer

Ligands

26 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: Q.289, V.290, D.291 Chain C: H.24 Ligand excluded by PLIP SO4.3: 3 residues within 4Å: Chain A: H.8, H.9, H.10 Ligand excluded by PLIP SO4.4: 3 residues within 4Å: Chain A: R.614, K.627, R.628 Ligand excluded by PLIP SO4.5: 4 residues within 4Å: Chain A: P.646, P.647, L.648 Chain D: H.243 Ligand excluded by PLIP SO4.6: 4 residues within 4Å: Chain A: T.673, S.674, T.675, A.676 Ligand excluded by PLIP SO4.11: 4 residues within 4Å: Chain B: P.275, G.309, Q.310, V.311 Ligand excluded by PLIP SO4.12: 3 residues within 4Å: Chain B: V.290, D.291 Chain D: H.24 Ligand excluded by PLIP SO4.13: 4 residues within 4Å: Chain B: P.646, P.647, L.648 Chain C: H.243 Ligand excluded by PLIP SO4.14: 4 residues within 4Å: Chain B: T.673, 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 SO4.20: 2 residues within 4Å: Chain B: H.8, H.9 Ligand excluded by PLIP SO4.21: 1 residues within 4Å: Chain C: R.382 Ligand excluded by PLIP SO4.22: 3 residues within 4Å: Chain C: S.163, R.164, N.249 Ligand excluded by PLIP SO4.23: 2 residues within 4Å: Chain C: R.195, L.201 Ligand excluded by PLIP SO4.24: 2 residues within 4Å: Chain C: P.193, R.195 Ligand excluded by PLIP SO4.25: 5 residues within 4Å: Chain C: H.43, P.44, D.45, L.46, Q.278 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 SO4.30: 2 residues within 4Å: Chain C: Y.186, R.378 Ligand excluded by PLIP SO4.31: 3 residues within 4Å: Chain D: N.380, R.382, R.402 Ligand excluded by PLIP SO4.32: 2 residues within 4Å: Chain D: R.195, L.201 Ligand excluded by PLIP SO4.33: 2 residues within 4Å: Chain D: P.193, R.195 Ligand excluded by PLIP SO4.34: 3 residues within 4Å: Chain D: S.163, R.164, N.249 Ligand excluded by PLIP SO4.35: 5 residues within 4Å: Chain D: H.43, P.44, D.45, L.46, Q.278 Ligand excluded by PLIP SO4.36: 1 residues within 4Å: Chain D: R.382 Ligand excluded by PLIP

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 3 residues within 4Å: Chain A: G.725, D.726, R.727 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.726, A:D.726, A:R.727, A:R.727 GOL.10: 6 residues within 4Å: Chain A: M.46, G.84, M.89, T.103, V.104, F.303 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.46, A:D.85 GOL.16: 2 residues within 4Å: Chain B: D.27, A.28 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.28 GOL.19: 7 residues within 4Å: Chain B: M.46, G.84, D.85, M.89, T.103, V.104, I.107 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.85

6 x COA: COENZYME A(Non-covalent)

COA.8: 18 residues within 4Å: Chain A: 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 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:A.82, A:L.130 Hydrogen bonds: A:A.82, A:G.84, A:V.86, A:K.87, A:R.191, A:R.191, A:Q.324 Salt bridges: A:K.87 pi-Stacking: A:F.320, A:F.320 COA.9: 7 residues within 4Å: Chain A: F.176, N.180, S.184, V.185, K.196, E.199, I.200 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.180, A:S.184, A:K.196, A:E.199 Salt bridges: A:K.196 COA.17: 17 residues within 4Å: Chain B: 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 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:A.82, B:L.130 Hydrogen bonds: B:A.82, B:G.84, B:D.85, B:V.86, B:K.87, B:K.87, B:R.191, B:R.191, B:Q.324 Salt bridges: B:K.87 pi-Stacking: B:F.320, B:F.320 COA.18: 7 residues within 4Å: Chain B: F.176, N.180, S.184, V.185, K.196, E.199, I.200 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.180, B:N.180, B:S.184, B:K.196, B:E.199 Salt bridges: B:K.196 COA.28: 20 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, F.330, H.359, L.361 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:A.224, C:F.225, C:F.225 Hydrogen bonds: C:Q.149, C:Q.175, C:R.210, C:R.210, C:T.213, C:S.258 pi-Cation interactions: C:R.210, C:R.210 COA.37: 19 residues within 4Å: Chain D: K.19, 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, F.330, H.359, L.361 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:A.224, 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 Salt bridges: D:K.19, D:K.19 pi-Cation interactions: D:R.210

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

PAP.29: 3 residues within 4Å: Chain B: Q.645 Chain C: Y.242, W.244 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B pi-Stacking: C:W.244, C:W.244, C:W.244 Hydrogen bonds: B:Q.645

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.38: 3 residues within 4Å: Chain A: Q.645 Chain D: Y.242, W.244 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain D Hydrogen bonds: A:Q.645 pi-Stacking: D:W.244, D:W.244, D:W.244, D:W.244

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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