SMTL ID : 3b1c.2 (1 other biounit)

Crystal structure of betaC-S lyase from Streptococcus anginosus: Internal aldimine form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

homo-dimer

Ligands

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

PLP.1: 12 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 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.123, A:I.205, A:I.205, A:K.238 Hydrogen bonds: A:V.98, A:V.99, A:N.175 Water bridges: A:Y.123, A:K.246, B:E.272 Salt bridges: A:K.246 pi-Stacking: A:Y.123 PLP.7: 11 residues within 4Å: Chain A: Y.64 Chain B: G.97, V.98, V.99, Y.123, C.171, N.175, D.203, I.205, H.206, K.238 16 PLIP interactions: 15 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.123, B:I.205, B:I.205, B:K.238 Hydrogen bonds: B:V.98, B:V.99, B:N.175, A:Y.64 Water bridges: B:T.237, B:K.238, B:K.246, B:K.246, B:K.246, B:K.246 Salt bridges: B:K.246 pi-Stacking: B:Y.123

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

SO4.2: 5 residues within 4Å: Chain A: I.38, A.39, Y.123, N.355, R.369 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:A.39, A:Y.123, A:N.355 Water bridges: A:Y.123, A:R.369, A:R.369, A:R.369 Salt bridges: A:R.369 SO4.8: 5 residues within 4Å: Chain B: I.38, A.39, Y.123, N.355, R.369 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:A.39, B:N.355 Water bridges: B:Y.123, B:Y.360, B:R.369, B:R.369 Salt bridges: B:R.369 SO4.9: 4 residues within 4Å: Chain B: A.127, R.131, L.137, S.139 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.139 Water bridges: B:R.131, B:S.139, B:S.362 Salt bridges: B:R.131

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: T.338, D.339, E.365 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.339, A:E.365 Water bridges: A:T.338, A:D.339, A:D.340 GOL.4: 4 residues within 4Å: Chain A: E.82, K.289, L.292, K.296 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.296, A:K.296 Water bridges: A:E.82, A:K.296 GOL.5: 2 residues within 4Å: Chain A: K.262, H.263 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.263 Water bridges: A:H.263, A:H.263 GOL.6: 5 residues within 4Å: Chain A: Q.32, Q.349, A.350, K.351, R.385 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.32 GOL.10: 3 residues within 4Å: Chain B: T.338, D.339, E.365 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:D.339, B:E.365, B:E.365 Water bridges: B:T.338, B:D.340, B:E.365, B:E.365 GOL.11: 6 residues within 4Å: Chain B: D.77, W.78, S.81, E.82, Y.285, K.289 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.81, B:S.81 Water bridges: B:W.78, B:Y.285 GOL.12: 4 residues within 4Å: Chain B: L.72, I.92, V.93, F.94 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.94

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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