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

Crystal structure of a benzoate coenzyme A ligase with Benzoyl-AMP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x BEZ: BENZOIC ACID(Non-covalent)

BEZ.1: 8 residues within 4Å: Chain A: A.221, P.251, V.256, F.272, G.274, A.275, G.278, M.282 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.221, A:P.251, A:V.256, A:F.272 Hydrogen bonds: A:A.275

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 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.4: 7 residues within 4Å: Chain A: R.297, L.298, A.299, L.320, D.321, V.323, P.340 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:A.299, A:A.299, A:D.321, A:D.321, A:D.321 Water bridges: A:R.297 GOL.5: 8 residues within 4Å: Chain A: S.182, G.183, S.184, T.185, G.186, R.187, P.188, S.434 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.182, A:G.183, A:R.187 Water bridges: A:K.189, A:K.494 GOL.6: 6 residues within 4Å: Chain A: P.10, K.12, F.13, N.14, E.17, H.18 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.12, A:N.14, A:N.14 GOL.7: 6 residues within 4Å: Chain A: L.71, T.95, L.96, K.223, G.248, R.250 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.95, A:T.95, A:G.248 Water bridges: A:R.250 GOL.8: 6 residues within 4Å: Chain A: Y.418, R.421, M.425, L.426, K.427, T.463 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.418, A:R.421, A:K.427, A:K.427, A:T.463, A:T.463 Water bridges: A:T.463

1 x OOB: 5'-O-[(R)-(benzoyloxy)(hydroxy)phosphoryl]adenosine(Non-covalent)

OOB.3: 22 residues within 4Å: Chain A: A.227, Y.228, A.302, G.303, E.304, A.305, D.324, G.325, I.326, G.327, S.328, T.329, L.332, H.333, I.334, S.404, D.406, Y.408, Y.418, R.421, K.427, Y.432 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:A.227, A:Y.228, A:A.302, A:I.334 Hydrogen bonds: A:G.303, A:D.324, A:G.327, A:T.329, A:T.329, A:D.406, A:Y.408, A:R.421, A:Y.432 Water bridges: A:S.181, A:S.404, A:Y.432 Salt bridges: A:K.427, A:K.427 pi-Stacking: A:H.333, A:Y.418

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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