SMTL ID : 1ycl.1

Crystal Structure of B. subtilis LuxS in Complex with a Catalytic 2-Ketone Intermediate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

CO.1: 5 residues within 4Å: Chain A: H.53, H.57, C.125, G.126 Ligands: KRI.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.53, A:H.57, A:C.125 CO.4: 5 residues within 4Å: Chain B: H.53, H.57, C.125, G.126 Ligands: KRI.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.53, B:H.57, B:C.125

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

SO4.2: 2 residues within 4Å: Chain A: K.48, R.138 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.138 Water bridges: A:D.132 Salt bridges: A:K.48 SO4.5: 2 residues within 4Å: Chain B: K.48, R.138 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.138 Salt bridges: B:K.48

2 x KRI: (S)-2-AMINO-4-[(2S,3R)-2,3,5-TRIHYDROXY-4-OXO-PENTYL]MERCAPTO-BUTYRIC ACID(Non-covalent)

KRI.3: 18 residues within 4Å: Chain A: H.53, E.56, H.57, R.64, D.77, I.78, S.79, C.125, G.126 Chain B: V.3, S.5, F.6, H.10, R.38, G.82, A.83, Y.88 Ligands: CO.1 15 PLIP interactions: 7 interactions with chain A, 8 interactions with chain B Hydrogen bonds: A:E.56, A:D.77, A:I.78, A:I.78, A:G.126, B:S.5, B:R.38, B:R.38, B:G.82, B:A.83 Water bridges: A:E.56, B:S.5, B:D.36 Salt bridges: A:R.64, B:K.34 KRI.6: 18 residues within 4Å: Chain A: V.3, S.5, F.6, H.10, R.38, G.82, A.83, Y.88 Chain B: H.53, E.56, H.57, R.64, D.77, I.78, S.79, C.125, G.126 Ligands: CO.4 15 PLIP interactions: 9 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:S.5, A:R.38, A:R.38, A:G.82, A:A.83, A:Y.88, B:E.56, B:D.77, B:I.78, B:I.78, B:G.126 Water bridges: A:S.5, A:D.36 Salt bridges: A:K.34, B:R.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rajan, R. et al., Crystal Structure of S-Ribosylhomocysteinase (LuxS) in Complex with a Catalytic 2-Ketone Intermediate. Biochemistry (2005)

Release Date

2005-03-15

Peptides

S-ribosylhomocysteinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

S-ribosylhomocysteinase