SMTL ID : 6c2q.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.17 Å

Oligo State

homo-dimer

Ligands

2 x EVM: L-Serine, N-[[3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]-4-pyridinyl]methylene](Non-covalent)

EVM.1: 21 residues within 4Å: Chain A: K.75, T.103, S.104, G.105, N.106, T.107, Q.179, A.217, G.218, T.219, G.220, G.221, T.222, E.266, G.267, I.268, Y.270, S.311, P.340, D.341, Y.346 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:I.268 Hydrogen bonds: A:T.103, A:S.104, 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:Y.270, A:Y.270, A:S.311 Water bridges: A:N.185, A:N.185, A:I.223 Salt bridges: A:K.75, A:K.75 EVM.12: 21 residues within 4Å: Chain B: K.75, T.103, S.104, G.105, N.106, T.107, Q.179, A.217, G.218, T.219, G.220, G.221, T.222, E.266, G.267, I.268, Y.270, S.311, P.340, D.341, Y.346 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:I.268 Hydrogen bonds: B:S.104, 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:Y.270, B:S.311 Water bridges: 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 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:N.205, A:D.208, A:D.208 CA.13: 3 residues within 4Å: Chain B: N.205, D.208, N.209 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:N.205, B:D.208, B:D.208

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

NA.3: 1 residues within 4Å: Chain A: G.142 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:G.142, B:R.369 NA.14: 1 residues within 4Å: Chain B: G.142 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.142 Water bridges: A:R.369

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.15: 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: 10 residues within 4Å: Chain A: L.67, Y.68, L.307, S.342 Chain B: L.67, N.69, P.70, G.72, R.344 Ligands: PEG.16 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:L.67, A:S.342, A:S.342, B:R.344 PEG.6: 4 residues within 4Å: Chain A: M.183, E.187, Y.190, K.228 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.228 Water bridges: A:K.228 PEG.16: 10 residues within 4Å: Chain A: L.67, N.69, P.70, G.72, R.344 Chain B: L.67, Y.68, L.307, S.342 Ligands: PEG.5 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.344, B:L.67, B:S.342, B:S.342 PEG.17: 4 residues within 4Å: Chain B: M.183, E.187, Y.190, K.228 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.228 Water bridges: B:K.228

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

PGE.7: 5 residues within 4Å: Chain A: S.81, E.187, A.188, F.191, G.192 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.187 PGE.8: 7 residues within 4Å: Chain A: F.207, D.208, L.210, R.211, N.234, K.236, I.237 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.211, A:R.211, A:N.234 PGE.18: 5 residues within 4Å: Chain B: S.81, E.187, A.188, F.191, G.192 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.187, B:E.187 PGE.19: 7 residues within 4Å: Chain B: F.207, D.208, L.210, R.211, N.234, K.236, I.237 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.211, B:R.211, B:N.234

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

EDO.9: 3 residues within 4Å: Chain A: R.121, E.144, I.146 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.121, A:E.144 EDO.10: 3 residues within 4Å: Chain A: P.274, Q.275, L.277 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.274 EDO.11: 3 residues within 4Å: Chain A: E.85, N.182, M.184 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.85 Water bridges: A:R.91, A:M.183 EDO.20: 3 residues within 4Å: Chain B: R.121, E.144, I.146 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.121 EDO.21: 3 residues within 4Å: Chain B: P.274, Q.275, L.277 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.274 EDO.22: 3 residues within 4Å: Chain B: E.85, N.182, M.184 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.85 Water bridges: B:R.91, B:M.183

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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