SMTL ID : 3b1e.2 (1 other biounit)

Crystal structure of betaC-S lyase from Streptococcus anginosus in complex with L-serine: alpha-Aminoacrylate form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

homo-dimer

Ligands

2 x 0JO: 2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid(Non-covalent)

0JO.1: 17 residues within 4Å: Chain A: I.38, A.39, G.97, V.98, V.99, P.100, Y.123, F.126, C.171, N.175, D.203, I.205, H.206, K.238, R.369 Chain B: Y.64 Ligands: EPE.8 20 PLIP interactions: 18 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:A.39, A:Y.123, A:F.126, A:I.205, B:Y.64 Hydrogen bonds: A:A.39, A:V.98, A:V.99, A:N.175 Water bridges: A:Y.123, A:T.237, A:T.237, A:K.246, A:N.355, A:R.369, A:R.369, B:Y.64 Salt bridges: A:K.246, A:R.369 pi-Stacking: A:Y.123 0JO.7: 17 residues within 4Å: Chain A: Y.64 Chain B: I.38, A.39, G.97, V.98, V.99, P.100, Y.123, F.126, C.171, N.175, D.203, I.205, H.206, K.238, R.369 Ligands: EPE.2 25 PLIP interactions: 22 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:A.39, B:Y.123, B:F.126, B:I.205, B:I.205, A:Y.64 Hydrogen bonds: B:A.39, B:V.98, B:V.99, B:N.175, A:Y.64 Water bridges: B:T.237, B:T.237, B:T.237, B:K.238, B:K.246, B:K.246, B:N.355, B:N.355, B:Y.360, B:R.369, A:Y.64 Salt bridges: B:K.246, B:R.369 pi-Stacking: B:Y.123

6 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.2: 9 residues within 4Å: Chain A: Y.64, E.272 Chain B: Y.22, W.37, I.38, V.99, Y.123 Ligands: 0JO.7, EPE.9 3 PLIP interactions: 3 interactions with chain A Water bridges: A:E.272 Salt bridges: A:E.272, A:E.272 EPE.3: 3 residues within 4Å: Chain A: D.340, F.343, R.356 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.340, A:R.356 Salt bridges: A:D.340, A:D.340 EPE.4: 4 residues within 4Å: Chain A: P.124, P.125, D.359 Ligands: EPE.8 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.128, A:N.355, A:N.355 Salt bridges: A:D.359, A:D.359 EPE.8: 9 residues within 4Å: Chain A: Y.22, W.37, I.38, V.99, Y.123 Chain B: Y.64, E.272 Ligands: 0JO.1, EPE.4 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Salt bridges: B:E.272, B:E.272 Water bridges: A:Y.123 EPE.9: 4 residues within 4Å: Chain B: P.124, P.125, D.359 Ligands: EPE.2 7 PLIP interactions: 7 interactions with chain B Water bridges: B:R.128, B:R.128, B:N.355, B:N.355, B:Y.360 Salt bridges: B:D.359, B:D.359 EPE.10: 3 residues within 4Å: Chain B: D.88, K.89, E.90 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.90 Water bridges: B:K.89, B:K.89 Salt bridges: B:D.88

2 x NA: SODIUM ION(Non-functional Binders)

NA.5: 1 residues within 4Å: Chain A: S.362 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.362 NA.11: 1 residues within 4Å: Chain B: S.362 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.362, B:S.362

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.6: 4 residues within 4Å: Chain A: Q.51, H.54, E.58 Chain B: H.54 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.51, A:H.54 Salt bridges: A:H.54, B:H.54

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kezuka, Y. et al., Structural insights into catalysis by beta C-S lyase from Streptococcus anginosus. Proteins (2012)

Release Date

2012-06-27

Peptides

BetaC-S lyase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

BetaC-S lyase

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