SMTL ID : 5flg.1

Crystal structure of the 6-carboxyhexanoate-CoA ligase (BioW)from Bacillus subtilis in complex with AMPPNP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.04 Å

Oligo State

homo-dimer

Ligands

2 x PML: PIMELIC ACID(Non-covalent)

PML.1: 11 residues within 4Å: Chain A: R.171, I.172, A.175, C.193, S.195, D.197, Y.200, T.202, Y.212, R.214 Ligands: ANP.2 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:A.175, A:Y.200 Hydrogen bonds: A:S.195, A:Y.200, A:Y.212 Salt bridges: A:R.171, A:R.214 PML.5: 10 residues within 4Å: Chain B: R.171, I.172, S.195, D.197, Y.200, T.202, Y.204, Y.212, R.214 Ligands: ANP.6 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.204 Hydrogen bonds: B:Y.200 Salt bridges: B:R.171, B:R.214

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.2: 23 residues within 4Å: Chain A: H.27, S.29, G.30, E.32, K.50, H.54, V.123, R.124, G.125, A.126, V.145, R.146, V.147, M.150, L.178, W.194, S.195, D.196, D.197, R.228 Ligands: PML.1, MG.3, MG.4 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:G.30, A:K.50, A:K.50, A:V.123, A:R.146, A:R.146, A:V.147, A:V.147, A:D.196, A:D.196, A:D.197, A:R.228 Water bridges: A:H.27, A:I.28, A:K.50, A:R.228, A:R.228 pi-Cation interactions: A:R.146, A:R.228 ANP.6: 22 residues within 4Å: Chain B: H.27, S.29, G.30, E.32, K.50, H.54, V.123, R.124, G.125, A.126, V.145, R.146, V.147, M.150, L.178, S.195, D.196, D.197, R.228 Ligands: PML.5, MG.7, MG.8 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:G.30, B:K.50, B:K.50, B:K.50, B:V.123, B:R.146, B:R.146, B:V.147, B:V.147, B:D.196, B:R.228 Water bridges: B:H.27, B:I.28, B:E.32, B:E.32, B:E.32, B:E.32, B:R.228, B:R.228 pi-Cation interactions: B:R.146, B:R.228

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: G.30 Ligands: ANP.2 No protein-ligand interaction detected (PLIP) MG.4: 4 residues within 4Å: Chain A: H.54, D.196, D.197 Ligands: ANP.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.196, A:D.197, H2O.1, H2O.2 MG.7: 2 residues within 4Å: Chain B: G.30 Ligands: ANP.6 No protein-ligand interaction detected (PLIP) MG.8: 4 residues within 4Å: Chain B: H.54, D.196, D.197 Ligands: ANP.6 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.196, B:D.197, H2O.2, H2O.3

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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