SMTL ID : 6c4p.1

Crystal Structures of Cystathionine beta-Synthase from Saccharomyces cerevisiae: the Structure of the PMP Complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x PMP: 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE(Non-covalent)

PMP.1: 17 residues within 4Å: Chain A: K.75, S.104, 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, Y.346 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:I.268 Hydrogen bonds: A:S.104, A:S.104, 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:S.104, A:N.106, A:N.185, A:N.185, A:I.223 Salt bridges: A:K.75 PMP.10: 17 residues within 4Å: Chain B: K.75, S.104, 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, Y.346 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:I.268 Hydrogen bonds: B:S.104, B:S.104, 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:S.104, B:N.106, B:N.185, B:T.219, B:I.223 Salt bridges: B:K.75

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 3 residues within 4Å: Chain A: N.205, D.208, N.209 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:N.205, A:D.208, A:D.208, H2O.2 CA.11: 3 residues within 4Å: Chain B: N.205, D.208, N.209 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:N.205, B:D.208, B:D.208, H2O.6

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

NA.3: 1 residues within 4Å: Chain A: G.142 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.122 NA.12: 1 residues within 4Å: Chain B: G.142 1 PLIP interactions: 1 interactions with chain B Water bridges: B:T.122

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

CL.4: 4 residues within 4Å: Chain A: K.129, M.130, G.267, I.268 Ligand excluded by PLIP CL.13: 4 residues within 4Å: Chain B: K.129, M.130, G.267, I.268 Ligand excluded by PLIP

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

PEG.5: 3 residues within 4Å: Chain A: S.81, A.188, F.191 No protein-ligand interaction detected (PLIP) PEG.6: 4 residues within 4Å: Chain A: P.186, E.187, Y.190, K.228 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.228 PEG.14: 3 residues within 4Å: Chain B: S.81, A.188, F.191 No protein-ligand interaction detected (PLIP) PEG.15: 4 residues within 4Å: Chain B: P.186, E.187, Y.190, K.228 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.228

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

EDO.7: 1 residues within 4Å: Chain A: E.144 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.144 EDO.8: 7 residues within 4Å: Chain A: P.244, F.245, I.260, Y.263, T.288, D.289, D.290 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:F.245, A:T.288, A:D.289, A:D.290, A:D.290 EDO.9: 8 residues within 4Å: Chain A: L.67, L.307 Chain B: L.67, N.69, P.70, G.72, R.344 Ligands: EDO.18 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.344 EDO.16: 1 residues within 4Å: Chain B: E.144 No protein-ligand interaction detected (PLIP) EDO.17: 7 residues within 4Å: Chain B: P.244, F.245, I.260, Y.263, T.288, D.289, D.290 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:F.245, B:T.288, B:D.290, B:D.290 EDO.18: 8 residues within 4Å: Chain A: L.67, N.69, P.70, G.72, R.344 Chain B: L.67, L.307 Ligands: EDO.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.344

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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