SMTL ID : 4rlf.2 (1 other biounit)

Crystal structure of a benzoate coenzyme A ligase with p-Toluic acid and o-Toluic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

monomer

Ligands

1 x 3SK: 2-methylbenzoic acid(Non-covalent)

3SK.1: 13 residues within 4Å: Chain A: A.222, Y.223, A.297, G.298, G.320, I.321, G.322, S.323, T.324, L.327, H.328, I.329, K.422 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:A.222, A:Y.223, A:A.297, A:I.329 Hydrogen bonds: A:G.298, A:G.320, A:G.322 Water bridges: A:E.299, A:K.422 Salt bridges: A:K.422 pi-Stacking: A:H.328

1 x 4MA: 4-METHYLBENZOIC ACID(Non-covalent)

4MA.2: 9 residues within 4Å: Chain A: A.216, P.246, T.247, P.248, G.269, A.270, G.273, M.277 Ligands: GOL.3 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.216, A:P.246, A:P.248 Hydrogen bonds: A:A.270

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 10 residues within 4Å: Chain A: A.217, F.221, Y.223, G.269, A.270, A.297, G.298, S.424, G.425 Ligands: 4MA.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.270 Water bridges: A:G.425 GOL.4: 9 residues within 4Å: Chain A: S.177, G.178, S.179, T.180, G.181, R.182, P.183, S.429, E.432 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.178, A:R.182 Water bridges: A:S.429 GOL.5: 7 residues within 4Å: Chain A: R.292, L.293, A.294, L.315, D.316, V.318, P.335 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.294, A:A.294, A:D.316, A:D.316 GOL.6: 8 residues within 4Å: Chain A: D.29, I.31, S.32, G.68, T.69, D.70, R.137 Ligands: GOL.7 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.29, A:S.32, A:T.69, A:T.69, A:D.70 Water bridges: A:G.68, A:S.136 GOL.7: 9 residues within 4Å: Chain A: D.70, V.135, S.136, R.137, P.138, D.148, F.149, A.150 Ligands: GOL.6 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.70, A:V.135, A:R.137, A:F.149, A:A.150 GOL.8: 8 residues within 4Å: Chain A: L.66, T.90, L.91, K.218, G.243, E.244, R.245, P.246 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.90, A:T.90

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thornburg, C.K. et al., Kinetically and Crystallographically Guided Mutations of a Benzoate CoA Ligase (BadA) Elucidate Mechanism and Expand Substrate Permissivity. Biochemistry (2015)

Release Date

2015-09-30

Peptides

Benzoate-coenzyme A ligase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Benzoate-coenzyme A ligase

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