SMTL ID : 5fm0.1

Crystal structure of the 6-carboxyhexanoate-CoA ligase (BioW)from Bacillus subtilis (PtCl4 derivative)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.44 Å

Oligo State

homo-dimer

Ligands

2 x WAQ: PIMELOYL-AMP(Non-covalent)

WAQ.1: 24 residues within 4Å: Chain A: E.32, V.123, R.124, G.125, A.126, V.145, R.146, V.147, R.171, I.172, L.178, C.193, S.195, D.196, D.197, Y.200, T.202, Y.204, Y.212, R.214, R.228 Ligands: PPV.2, MG.3, MG.4 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Y.200, A:Y.204 Hydrogen bonds: A:G.125, A:V.147, A:V.147, A:D.196, A:Y.200, A:Y.200, A:Y.212, A:R.228 Salt bridges: A:R.171, A:R.214, A:R.228, A:R.228 pi-Cation interactions: A:R.228 WAQ.8: 23 residues within 4Å: Chain B: E.32, V.123, R.124, G.125, A.126, V.145, R.146, V.147, R.171, I.172, L.178, C.193, W.194, S.195, D.196, D.197, Y.200, T.202, Y.204, Y.212, R.214, R.228 Ligands: PPV.9 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:Y.200, B:Y.204 Hydrogen bonds: B:G.125, B:V.147, B:V.147, B:D.196, B:D.196, B:D.196, B:Y.200, B:Y.212, B:R.228 Salt bridges: B:R.171, B:R.214, B:R.228, B:R.228 pi-Cation interactions: B:R.228

2 x PPV: PYROPHOSPHATE(Non-covalent)

PPV.2: 11 residues within 4Å: Chain A: H.27, S.29, G.30, K.50, H.54, R.146, D.196, D.197 Ligands: WAQ.1, MG.3, MG.4 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.30 Water bridges: A:E.32, A:K.50, A:R.146 Salt bridges: A:H.27, A:K.50, A:H.54, A:R.146 PPV.9: 9 residues within 4Å: Chain B: H.27, S.29, G.30, K.50, H.54, R.146, D.196, D.197 Ligands: WAQ.8 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:G.30, B:G.30, B:D.196 Salt bridges: B:H.27, B:K.50, B:K.50, B:H.54, B:R.146

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: E.174 Ligands: WAQ.1, PPV.2 No protein-ligand interaction detected (PLIP) MG.4: 5 residues within 4Å: Chain A: H.54, D.196, D.197 Ligands: WAQ.1, PPV.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.196, A:D.197, H2O.1

6 x PT: PLATINUM (II) ION(Non-covalent)

PT.5: 2 residues within 4Å: Chain A: M.17 Ligands: PT.7 No protein-ligand interaction detected (PLIP) PT.6: 2 residues within 4Å: Chain A: K.102, M.210 No protein-ligand interaction detected (PLIP) PT.7: 3 residues within 4Å: Chain A: M.17, N.18 Ligands: PT.5 No protein-ligand interaction detected (PLIP) PT.10: 3 residues within 4Å: Chain B: M.17, N.18, K.26 No protein-ligand interaction detected (PLIP) PT.11: 2 residues within 4Å: Chain B: K.102, M.210 No protein-ligand interaction detected (PLIP) PT.12: 2 residues within 4Å: Chain B: M.17, K.58 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, M. et al., Using the pimeloyl-CoA synthetase adenylation fold to synthesize fatty acid thioesters. Nat. Chem. Biol. (2017)

Release Date

2016-11-16

Peptides

6-CARBOXYHEXANOATE--COA LIGASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

6-CARBOXYHEXANOATE--COA LIGASE

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