SMTL ID : 3cw9.1

4-Chlorobenzoyl-CoA Ligase/Synthetase in the Thioester-forming Conformation, bound to 4-chlorophenacyl-CoA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: E.230, F.231 Ligands: 01A.4 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain B: E.230 Ligands: 01A.10 No protein-ligand interaction detected (PLIP)

3 x NO3: NITRATE ION(Non-functional Binders)

NO3.2: 7 residues within 4Å: Chain A: Y.160, H.207, G.409, E.410, N.411 Ligands: AMP.3, 01A.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.307, A:T.307, A:N.411 Water bridges: A:T.161 NO3.7: 7 residues within 4Å: Chain B: Y.160, H.207, G.409, E.410, N.411 Ligands: AMP.9, 01A.10 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.307, B:T.307, B:N.411 NO3.8: 2 residues within 4Å: Chain B: P.425, F.464 1 PLIP interactions: 1 interactions with chain B Water bridges: B:S.467

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.3: 19 residues within 4Å: Chain A: T.161, G.281, A.282, T.283, N.302, I.303, Y.304, G.305, T.306, T.307, E.308, M.324, T.383, D.385, R.400, I.406, N.411 Ligands: NO3.2, 01A.4 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:T.161, A:T.161, A:G.281, A:T.283, A:I.303, A:G.305, A:T.307, A:T.307, A:D.385, A:R.400, A:N.411 Water bridges: A:T.283, A:N.302, A:Y.381, A:T.383 pi-Stacking: A:Y.304, A:Y.304 AMP.9: 19 residues within 4Å: Chain B: T.161, G.281, A.282, T.283, N.302, I.303, Y.304, G.305, T.306, T.307, E.308, M.324, T.383, D.385, R.400, I.406, N.411 Ligands: NO3.7, 01A.10 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:T.161, B:T.161, B:G.281, B:I.303, B:G.305, B:T.307, B:E.308, B:T.383, B:D.385, B:R.400, B:N.411 Water bridges: B:T.283, B:M.284, B:N.302, B:D.385

2 x 01A: 4-Chlorophenacyl-coenzyme A(Non-covalent)

01A.4: 30 residues within 4Å: Chain A: R.87, F.184, M.203, P.204, H.207, V.208, V.209, F.231, T.251, T.253, H.254, A.280, G.281, I.303, G.305, T.306, T.307, M.310, N.311, S.407, G.408, G.409, E.410, W.440, F.473, R.475, K.477 Ligands: MG.1, NO3.2, AMP.3 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:V.208, A:V.209, A:T.253, A:A.280 Hydrogen bonds: A:S.407, A:G.408, A:G.409, A:R.475, A:K.477 Water bridges: A:R.87, A:R.87, A:F.231, A:R.475 Salt bridges: A:R.87, A:R.87, A:R.475 pi-Stacking: A:W.440 01A.10: 30 residues within 4Å: Chain B: R.87, F.184, M.203, P.204, H.207, V.208, V.209, F.231, T.251, T.253, H.254, A.280, G.281, I.303, G.305, T.306, T.307, M.310, N.311, S.407, G.408, G.409, E.410, W.440, F.473, R.475, K.477 Ligands: MG.6, NO3.7, AMP.9 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:V.208, B:V.209, B:T.253, B:A.280 Hydrogen bonds: B:R.87, B:S.407, B:G.408, B:G.409, B:R.475, B:K.477 Water bridges: B:F.231, B:E.410, B:E.410, B:R.475 Salt bridges: B:R.87, B:R.475 pi-Stacking: B:W.440

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 4 residues within 4Å: Chain A: N.5, L.8, R.36, L.72 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.5 Water bridges: A:H.32

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Reger, A.S. et al., Structural characterization of a 140 degrees domain movement in the two-step reaction catalyzed by 4-chlorobenzoate:CoA ligase. Biochemistry (2008)

Release Date

2008-09-02

Peptides

4-chlorobenzoyl CoA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

4-chlorobenzoyl CoA ligase

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