SMTL ID : 6vju.1

Crystal Structure of Cystathionine beta synthase from Legionella pneumophila with LLP, PLP, and homocysteine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 3 residues within 4Å: Chain A: L.15, A.16, Y.56 2 PLIP interactions: 2 interactions with chain A Water bridges: A:A.16, A:Y.56 EDO.2: 6 residues within 4Å: Chain A: E.103, K.104, M.105, S.106, R.122, K.311 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.103, A:R.122, A:K.311, A:K.311 EDO.3: 3 residues within 4Å: Chain A: N.162, Y.165, K.198 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.162, A:K.198 Water bridges: A:N.162, A:Y.165, A:Y.165, A:Y.165, A:K.198 EDO.6: 5 residues within 4Å: Chain A: H.20, T.21, P.22 Chain B: Y.11 Ligands: ACT.8 No protein-ligand interaction detected (PLIP) EDO.11: 5 residues within 4Å: Chain A: I.10 Chain B: D.175, F.176, D.179, K.296 No protein-ligand interaction detected (PLIP) EDO.12: 9 residues within 4Å: Chain B: S.79, K.104, M.105, V.230, E.231, G.232, I.233, G.234, Y.235 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.104, B:G.232, B:G.234 Water bridges: B:Y.235 EDO.13: 5 residues within 4Å: Chain B: L.219, G.220, G.221, N.244, Y.250 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.219, B:N.244, B:N.244 EDO.14: 4 residues within 4Å: Chain B: N.13, L.15, Y.56, L.93 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.13 EDO.15: 2 residues within 4Å: Chain A: D.174 Chain B: H.8 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:D.175 Hydrogen bonds: B:H.8 EDO.18: 4 residues within 4Å: Chain B: L.15, A.16, I.18, Y.56 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.16, B:I.18 Water bridges: B:E.57

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

ACT.4: 4 residues within 4Å: Chain A: L.219, G.220, G.221, N.244 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:N.244 Hydrogen bonds: A:L.219 Water bridges: A:N.244 ACT.5: 7 residues within 4Å: Chain A: K.51, T.78, S.79, G.80, N.81, T.82, Q.154 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.78, A:S.79, A:G.80, A:N.81, A:T.82, A:Q.154 Water bridges: A:N.81 ACT.7: 8 residues within 4Å: Chain A: T.17, G.19, H.20, T.21, P.22, F.44, N.45 Chain B: F.44 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.44 Hydrogen bonds: A:G.19, A:N.45 ACT.8: 6 residues within 4Å: Chain A: H.20, E.171, D.174, D.175 Chain B: H.8 Ligands: EDO.6 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:D.174 Salt bridges: A:H.20 ACT.10: 6 residues within 4Å: Chain A: F.43, F.44 Chain B: F.43, F.44, N.45, G.48 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.43 ACT.16: 8 residues within 4Å: Chain B: K.51, T.78, S.79, G.80, N.81, T.82, Q.154 Ligands: PLP.17 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:T.78, B:S.79, B:G.80, B:N.81, B:T.82, B:Q.154, B:Q.154 Salt bridges: B:K.51 ACT.19: 8 residues within 4Å: Chain A: F.44 Chain B: T.17, G.19, H.20, T.21, P.22, F.44, N.45 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.17, B:G.19 Hydrophobic interactions: A:F.44

1 x HCS: 2-AMINO-4-MERCAPTO-BUTYRIC ACID(Non-covalent)

HCS.9: 3 residues within 4Å: Chain A: G.220, Y.250, K.252 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.252 Hydrogen bonds: A:G.220 Water bridges: A:K.252, A:K.252

1 x PLP: PYRIDOXAL-5'-PHOSPHATE(Non-covalent)

PLP.17: 18 residues within 4Å: Chain B: K.51, S.79, N.81, G.186, V.187, G.188, T.189, G.190, G.191, T.192, E.231, G.232, I.233, S.276, P.302, D.303, Y.308 Ligands: ACT.16 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:N.81, B:G.186, B:G.188, B:T.189, B:G.190, B:G.191, B:T.192, B:T.192, B:S.276 Water bridges: B:S.79, B:N.81, B:N.160, B:T.192, B:I.193, B:E.231, B:Y.308 Salt bridges: B:K.51

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bolejack, M.J. et al., Crystal Structure of Cystathionine beta synthase from Legionella pneumophila with LLP, PLP, and homocysteine. to be published

Release Date

2020-02-05

Peptides

Cystathionine beta-lyase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cystathionine beta-lyase