SMTL ID : 3b1d.2 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.66 Å

Oligo State

homo-dimer

Ligands

1 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)

PLP.1: 14 residues within 4Å: Chain A: G.97, V.98, V.99, P.100, Y.123, C.171, N.175, D.203, I.205, H.206, K.238 Chain B: Y.64 Ligands: PLS.2, EPE.8 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.123, A:N.175, A:I.205, A:I.205, A:K.238 Hydrogen bonds: A:V.98, A:V.99, A:N.175 Water bridges: A:K.238, A:K.246 Salt bridges: A:K.246 pi-Stacking: A:Y.123

2 x PLS: [3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-SERINE(Covalent)(Non-covalent)

PLS.2: 16 residues within 4Å: Chain A: I.38, A.39, G.97, V.98, V.99, Y.123, C.171, N.175, D.203, I.205, H.206, K.238, R.369 Chain B: Y.64 Ligands: PLP.1, EPE.8 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:Y.123, A:I.205, A:I.205 Hydrogen bonds: A:A.39, A:V.98, A:V.99, A:Y.123, A:Y.123, A:N.175, A:K.238 Water bridges: A:T.237, A:K.246, A:R.369, A:R.369, A:R.369 Salt bridges: A:K.238, A:K.246, A:R.369 pi-Stacking: A:Y.123 PLS.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, C.171, N.175, D.203, I.205, H.206, K.238, R.369 Ligands: EPE.3, EPE.9 23 PLIP interactions: 21 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.123, B:I.205, B:I.205 Hydrogen bonds: B:A.39, B:V.98, B:V.99, B:Y.123, B:N.175, B:K.238, A:Y.64 Water bridges: B:T.237, B:T.237, B:K.246, B:K.246, B:K.246, B:N.355, B:Y.360, B:R.369, B:R.369, A:E.272 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.3: 9 residues within 4Å: Chain A: Y.64, E.272 Chain B: Y.22, W.37, I.38, V.99, Y.123 Ligands: PLS.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.4: 3 residues within 4Å: Chain A: D.340, F.343, R.356 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.356 Salt bridges: A:D.340, A:D.340 EPE.5: 4 residues within 4Å: Chain A: P.124, P.125, D.359 Ligands: EPE.8 7 PLIP interactions: 7 interactions with chain A Water bridges: A:R.128, A:N.355, A:N.355, A:Y.360, A:R.369 Salt bridges: A:D.359, A:D.359 EPE.8: 10 residues within 4Å: Chain A: Y.22, W.37, I.38, V.99, Y.123 Chain B: Y.64, E.272 Ligands: PLP.1, PLS.2, EPE.5 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:E.272, B:E.272 EPE.9: 5 residues within 4Å: Chain B: P.124, P.125, D.359 Ligands: EPE.3, PLS.7 6 PLIP interactions: 6 interactions with chain B Water bridges: B:R.128, B:R.128, B:Y.360, B:R.369 Salt bridges: B:D.359, B:D.359 EPE.10: 3 residues within 4Å: Chain B: D.88, K.89, E.90 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.90, 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.6: 1 residues within 4Å: Chain A: S.362 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.362 Water bridges: A:S.120, 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

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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