SMTL ID : 6c2z.1

Crystal Structures of Cystathionine beta-Synthase from Saccharomyces cerevisiae: the Structure of the PLP-Aminoacrylate Intermediate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.37 Å

Oligo State

homo-dimer

Ligands

2 x P1T: 2-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]ACRYLIC ACID(Non-covalent)

P1T.1: 21 residues within 4Å: Chain A: K.75, T.103, S.104, G.105, N.106, T.107, Q.179, 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, Y.346 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:T.219, A:I.268, A:P.340 Hydrogen bonds: A:T.103, A:S.104, A:G.105, A:N.106, A:N.106, A:T.107, A:T.107, A:Q.179, A:Q.179, A:G.218, A:T.219, A:T.219, A:T.219, A:G.220, A:G.221, A:T.222, A:T.222, A:S.311 Water bridges: A:S.104, A:N.185, A:N.185, A:I.223, A:Y.270 Salt bridges: A:K.75, A:K.75 P1T.15: 21 residues within 4Å: Chain B: K.75, T.103, S.104, G.105, N.106, T.107, Q.179, 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, Y.346 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:T.219, B:I.268, B:P.340 Hydrogen bonds: B:S.104, B:G.105, B:N.106, B:N.106, B:T.107, B:Q.179, B:Q.179, B:G.218, B:T.219, B:T.219, B:T.219, B:G.220, B:G.221, B:T.222, B:T.222, B:S.311 Water bridges: B:S.104, B:S.104, B:N.185, B:T.219, B:I.223 Salt bridges: B:K.75, B:K.75

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 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.11, H2O.11 CA.16: 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.24, H2O.25

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

NA.3: 1 residues within 4Å: Chain A: G.142 No protein-ligand interaction detected (PLIP) NA.17: 1 residues within 4Å: Chain B: G.142 No protein-ligand interaction detected (PLIP)

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

CL.4: 6 residues within 4Å: Chain A: K.129, M.130, V.265, E.266, G.267, I.268 Ligand excluded by PLIP CL.18: 6 residues within 4Å: Chain B: K.129, M.130, V.265, E.266, G.267, I.268 Ligand excluded by PLIP

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

PEG.5: 11 residues within 4Å: Chain A: L.67, Y.68, L.307 Chain B: L.67, Y.68, N.69, P.70, G.71, G.72, R.344 Ligands: PEG.19 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:L.67, B:G.71, B:R.344 PEG.6: 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.19: 11 residues within 4Å: Chain A: L.67, Y.68, N.69, P.70, G.71, G.72, R.344 Chain B: L.67, Y.68, L.307 Ligands: PEG.5 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:L.67, A:G.71, A:R.344 PEG.20: 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

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

PGE.7: 6 residues within 4Å: Chain A: S.81, M.184, E.187, A.188, F.191, G.192 No protein-ligand interaction detected (PLIP) PGE.21: 6 residues within 4Å: Chain B: S.81, M.184, E.187, A.188, F.191, G.192 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.187

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

EDO.8: 5 residues within 4Å: Chain A: R.211, K.236, Q.238, Y.322, L.329 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.211, A:Y.322, A:Y.322 EDO.9: 3 residues within 4Å: Chain A: K.264, K.349, W.355 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:K.264 Water bridges: A:K.264, A:K.264, A:K.349, A:W.355, A:W.355, A:K.358, A:N.359 EDO.10: 6 residues within 4Å: Chain A: R.211, E.328, L.329, T.330, D.332, D.333 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.328, A:D.332 Water bridges: A:D.332 EDO.11: 6 residues within 4Å: Chain A: F.207, D.208, L.210, R.211, N.234, I.237 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.211, A:R.211 EDO.12: 4 residues within 4Å: Chain A: F.245, K.257, T.258, I.260 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.258 Water bridges: A:I.260, A:D.289 EDO.13: 4 residues within 4Å: Chain A: I.248, D.271, F.272, V.273 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.273, A:V.273 EDO.14: 1 residues within 4Å: Chain A: P.327 No protein-ligand interaction detected (PLIP) EDO.22: 5 residues within 4Å: Chain B: R.211, K.236, Q.238, Y.322, L.329 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.211, B:Y.322 Water bridges: B:H.326 EDO.23: 3 residues within 4Å: Chain B: K.264, K.349, W.355 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:K.264 Water bridges: B:K.264, B:K.264, B:K.349, B:W.355, B:W.355, B:K.358, B:N.359 EDO.24: 6 residues within 4Å: Chain B: R.211, E.328, L.329, T.330, D.332, D.333 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.328, B:D.332 Water bridges: B:R.211 EDO.25: 6 residues within 4Å: Chain B: F.207, D.208, L.210, R.211, N.234, I.237 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.211, B:R.211 EDO.26: 4 residues within 4Å: Chain B: F.245, K.257, T.258, I.260 2 PLIP interactions: 2 interactions with chain B Water bridges: B:I.260, B:D.289 EDO.27: 4 residues within 4Å: Chain B: I.248, D.271, F.272, V.273 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.273, B:V.273 EDO.28: 1 residues within 4Å: Chain B: P.327 No protein-ligand interaction detected (PLIP)

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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