SMTL ID : 2fqt.1

Crystal structure of B.subtilis LuxS in complex with (2S)-2-Amino-4-[(2R,3S)-2,3-dihydroxy-3-N-hydroxycarbamoyl-propylmercapto]butyric acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.79 Å

Oligo State

homo-dimer

Ligands

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 2 residues within 4Å: Chain A: K.49, R.139 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.139, A:R.139, A:R.139 Salt bridges: A:K.49, A:R.139 SO4.2: 3 residues within 4Å: Chain A: N.122, E.123, A.129 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.123 Water bridges: A:K.124 SO4.5: 2 residues within 4Å: Chain B: K.49, R.139 5 PLIP interactions: 5 interactions with chain B Water bridges: B:R.139, B:R.139, B:R.139 Salt bridges: B:K.49, B:R.139 SO4.6: 3 residues within 4Å: Chain B: N.122, E.123, A.129 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.123 Water bridges: B:K.124

2 x CO: COBALT (II) ION(Non-covalent)

CO.3: 5 residues within 4Å: Chain A: H.54, H.58, C.126, G.127 Ligands: H1D.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.54, A:H.58, A:C.126 CO.7: 5 residues within 4Å: Chain B: H.54, H.58, C.126, G.127 Ligands: H1D.8 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.54, B:H.58, B:C.126

2 x H1D: (2S)-2-AMINO-4-[(2R,3S)-2,3-DIHYDROXY-3-N-HYDROXYCARBAMOYL-PROPYLMERCAPTO]BUTYRIC ACID(Non-covalent)

H1D.4: 17 residues within 4Å: Chain A: H.54, E.57, H.58, A.61, D.78, I.79, S.80, C.126, G.127 Chain B: S.6, F.7, H.11, K.35, R.39, C.84, Y.89 Ligands: CO.3 12 PLIP interactions: 8 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:Y.89 Hydrogen bonds: B:S.6, B:R.39, B:R.39, B:C.84, A:D.78, A:I.79, A:G.127 Water bridges: B:V.4, B:V.4, A:E.57 Salt bridges: B:K.35 H1D.8: 17 residues within 4Å: Chain A: S.6, F.7, H.11, K.35, R.39, C.84, Y.89 Chain B: H.54, E.57, H.58, A.61, D.78, I.79, S.80, C.126, G.127 Ligands: CO.7 13 PLIP interactions: 4 interactions with chain B, 9 interactions with chain A Hydrogen bonds: B:D.78, B:D.78, B:I.79, B:G.127, A:S.6, A:R.39, A:R.39, A:C.84, A:Y.89 Hydrophobic interactions: A:Y.89 Water bridges: A:V.4, A:Y.89 Salt bridges: A:K.35

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shen, G. et al., Design and Synthesis of Substrate Analogue Inhibitors of S-Ribosylhomocysteinase (LuxS). J.Med.Chem. (2006)

Release Date

2006-05-30

Peptides

S-ribosylhomocysteine lyase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

S-ribosylhomocysteine lyase

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