SMTL ID : 4rmn.3 (2 other biounits)

Crystal structure of a benzoate coenzyme A ligase with 2-Thiophene Carboxylic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

monomer

Ligands

2 x C21: THIOPHENE-2-CARBOXYLIC ACID(Non-covalent)

C21.1: 11 residues within 4Å: Chain A: A.227, Y.228, A.302, G.303, I.326, G.327, S.328, L.332, H.333, I.334, K.427 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.228, A:Y.228, A:A.302, A:I.334 Hydrogen bonds: A:G.303, A:G.327 Water bridges: A:E.304, A:K.427 Salt bridges: A:K.427 pi-Stacking: A:H.333 C21.2: 9 residues within 4Å: Chain A: A.221, A.222, F.226, Y.228, G.274, A.275, A.302, S.429, G.430 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.222 Hydrogen bonds: A:A.275 pi-Stacking: A:F.226

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 10 residues within 4Å: Chain A: S.182, G.183, S.184, T.185, G.186, R.187, P.188, S.434, E.437 Ligands: GOL.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.183, A:R.187 Water bridges: A:S.434, A:E.437 GOL.4: 6 residues within 4Å: Chain A: L.71, T.95, L.96, K.223, G.248, P.251 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.95, A:G.248 Water bridges: A:T.95, A:R.250 GOL.5: 7 residues within 4Å: Chain A: L.97, D.101, S.182, P.188, E.437, K.494 Ligands: GOL.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.182, A:S.182, A:K.494 GOL.6: 5 residues within 4Å: Chain A: I.357, E.358, L.359, R.410, Y.416 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.359, A:V.367, A:Y.416, A:Y.416 Water bridges: A:R.410 GOL.7: 8 residues within 4Å: Chain A: D.75, V.140, S.141, R.142, P.143, D.153, F.154, A.155 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.75, A:V.140, A:R.142, A:F.154, A:A.155 GOL.8: 5 residues within 4Å: Chain A: P.10, F.13, N.14, E.17, H.18 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.14, A:N.14, A:E.17 Water bridges: A:K.12

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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