SMTL ID : 6c2h.1

Crystal Structures of Cystathionine beta-Synthase from Saccharomyces cerevisiae: the Structure of the Catalytic Core

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.49 Å

Oligo State

homo-dimer

Ligands

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

PLP.1: 16 residues within 4Å: Chain A: K.75, N.106, G.216, A.217, G.218, T.219, G.220, G.221, T.222, E.266, G.267, I.268, S.311, P.340, D.341 Ligands: ACT.2 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:K.75, A:P.340 Hydrogen bonds: A:N.106, A:G.218, A:T.219, A:G.220, A:G.221, A:T.222, A:T.222, A:T.222, A:S.311 Water bridges: A:K.75, A:N.106, A:N.185, A:N.185, A:I.223, A:E.266 Salt bridges: A:K.75 PLP.13: 16 residues within 4Å: Chain B: K.75, N.106, G.216, A.217, G.218, T.219, G.220, G.221, T.222, E.266, G.267, I.268, S.311, P.340, D.341 Ligands: ACT.14 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:K.75, B:P.340 Hydrogen bonds: B:N.106, B:G.218, B:T.219, B:G.220, B:G.221, B:T.222, B:T.222, B:T.222, B:S.311 Water bridges: B:K.75, B:N.106, B:N.185, B:T.219, B:I.223, B:E.266 Salt bridges: B:K.75

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

ACT.2: 8 residues within 4Å: Chain A: K.75, T.103, S.104, G.105, N.106, T.107, Q.179 Ligands: PLP.1 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:T.103, A:S.104, A:G.105, A:N.106, A:T.107, A:T.107, A:Q.179 Salt bridges: A:K.75 ACT.14: 8 residues within 4Å: Chain B: K.75, T.103, S.104, G.105, N.106, T.107, Q.179 Ligands: PLP.13 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.104, B:G.105, B:N.106, B:T.107, B:Q.179 Water bridges: B:N.106 Salt bridges: B:K.75

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 3 residues within 4Å: Chain A: N.205, D.208, N.209 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:N.205, A:D.208, A:D.208, H2O.10, H2O.11 CA.15: 3 residues within 4Å: Chain B: N.205, D.208, N.209 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:N.205, B:D.208, B:D.208, H2O.23, H2O.24

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

NA.4: 1 residues within 4Å: Chain A: G.142 2 PLIP interactions: 2 interactions with chain A Water bridges: A:T.122, A:G.142 NA.16: 1 residues within 4Å: Chain B: G.142 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.142 Water bridges: B:T.122

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 6 residues within 4Å: Chain A: K.129, M.130, V.265, E.266, G.267, I.268 Ligand excluded by PLIP CL.17: 6 residues within 4Å: Chain B: K.129, M.130, V.265, E.266, G.267, I.268 Ligand excluded by PLIP

6 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 9 residues within 4Å: Chain A: L.67, Y.68, L.307, S.342 Chain B: L.67, N.69, P.70, G.72 Ligands: PEG.18 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Water bridges: B:R.344 Hydrogen bonds: A:L.67, A:L.307, A:S.342 PEG.7: 5 residues within 4Å: Chain A: M.183, P.186, E.187, Y.190, K.228 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.228 PEG.8: 4 residues within 4Å: Chain A: R.121, E.144, I.145, I.146 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.121 Water bridges: A:R.121, A:E.144, A:I.145 PEG.18: 9 residues within 4Å: Chain A: L.67, N.69, P.70, G.72 Chain B: L.67, Y.68, L.307, S.342 Ligands: PEG.6 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:L.67, B:L.307, B:S.342 Water bridges: A:R.344 PEG.19: 5 residues within 4Å: Chain B: M.183, P.186, E.187, Y.190, K.228 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.228 PEG.20: 4 residues within 4Å: Chain B: R.121, E.144, I.145, I.146 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.121 Water bridges: B:R.121, B:I.145

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.9: 4 residues within 4Å: Chain A: E.187, A.188, F.191, G.192 No protein-ligand interaction detected (PLIP) PGE.21: 4 residues within 4Å: Chain B: E.187, A.188, F.191, G.192 No protein-ligand interaction detected (PLIP)

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.10: 3 residues within 4Å: Chain A: K.264, K.349, W.355 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.264 Water bridges: A:K.264, A:K.349, A:W.355 EDO.11: 5 residues within 4Å: Chain A: R.211, E.328, L.329, T.330, D.333 No protein-ligand interaction detected (PLIP) EDO.12: 4 residues within 4Å: Chain A: F.245, K.257, T.258, I.260 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.258 Water bridges: A:D.259 EDO.22: 3 residues within 4Å: Chain B: K.264, K.349, W.355 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.264 Water bridges: B:K.264, B:K.349, B:W.355 EDO.23: 5 residues within 4Å: Chain B: R.211, E.328, L.329, T.330, D.333 No protein-ligand interaction detected (PLIP) EDO.24: 4 residues within 4Å: Chain B: F.245, K.257, T.258, I.260 1 PLIP interactions: 1 interactions with chain B Water bridges: B:D.259

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tu, Y. et al., Crystal Structures of Cystathionine beta-Synthase from Saccharomyces cerevisiae: One Enzymatic Step at a Time. Biochemistry (2018)

Release Date

2018-04-25

Peptides

Cystathionine beta-synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Cystathionine beta-synthase

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