SMTL ID : 7pyt.1

Benzoylsuccinyl-CoA thiolase with coenzyme A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-2-2-mer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.42, C.45, C.55, C.58 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.42, A:C.45, A:C.55, A:C.58 ZN.7: 4 residues within 4Å: Chain C: C.42, C.45, C.55, C.58 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.42, C:C.45, C:C.55, C:C.58

4 x PE8: 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL(Non-covalent)

PE8.2: 6 residues within 4Å: Chain A: K.73, D.97, L.98, P.99, D.118, E.120 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.73 PE8.6: 8 residues within 4Å: Chain B: D.42, P.44, L.69, G.70 Chain C: N.57, C.58, W.59 Ligands: MG.5 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.42 Water bridges: B:N.75 PE8.8: 13 residues within 4Å: Chain C: F.21, H.22, I.25, F.50, K.51, R.103, V.104, F.105 Chain D: R.129, S.130, D.131, I.132, M.135 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Water bridges: D:Y.244 Hydrogen bonds: C:F.105 PE8.11: 9 residues within 4Å: Chain D: K.2, L.3, R.5, E.6, K.233, V.234, A.235, S.268, V.387 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.2, D:E.6, D:K.233

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 3 residues within 4Å: Chain B: I.185, T.186, V.187 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.187 Water bridges: B:T.186, B:E.188 PO4.4: 3 residues within 4Å: Chain B: H.118, R.119 Chain D: R.129 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:R.119, D:R.129 Salt bridges: B:H.118

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 4 residues within 4Å: Chain B: R.43, P.44, D.45 Ligands: PE8.6 No protein-ligand interaction detected (PLIP)

1 x COA: COENZYME A(Non-covalent)

COA.9: 24 residues within 4Å: Chain C: I.82 Chain D: K.19, C.85, S.121, G.122, A.124, F.125, M.140, T.141, W.180, F.181, R.194, V.196, L.202, Q.203, C.205, C.206, G.207, I.208, H.281, A.283, F.284, H.331 Ligands: CL.10 23 PLIP interactions: 22 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:V.196, D:L.202, D:I.208, C:I.82 Hydrogen bonds: D:G.122, D:C.205, D:C.206, D:I.208 Water bridges: D:R.119, D:R.119, D:A.123, D:F.125, D:T.141, D:R.170, D:W.180, D:W.180, D:R.194, D:R.194, D:G.207 Salt bridges: D:K.19, D:K.19, D:R.194 pi-Stacking: D:F.181

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.10: 6 residues within 4Å: Chain D: Y.144, T.369, G.370, G.371, H.378 Ligands: COA.9 Ligand excluded by PLIP

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.12: 7 residues within 4Å: Chain D: R.170, F.181, K.182, A.184, I.185, T.186, E.189 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.170, D:K.182 Salt bridges: D:E.189

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Weidenweber, S. et al., Finis tolueni: a new type of thiolase with an integrated Zn-finger subunit catalyzes the final step of anaerobic toluene metabolism. Febs J. (2022)

Release Date

2022-04-06

Peptides

Benzoylsuccinyl-CoA thiolase subunit: AC
Benzoylsuccinyl-CoA thiolase subunit: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Benzoylsuccinyl-CoA thiolase subunit

Benzoylsuccinyl-CoA thiolase subunit

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