SMTL ID : 7lx1.1

The internal aldimine form of the wild-type Salmonella Typhimurium Tryptophan Synthase in complex with cesium ion at the metal coordination site at 1.61 Angstrom resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.61 Å

Oligo State

hetero-2-2-mer

Ligands

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

EDO.1: 6 residues within 4Å: Chain A: E.31, L.34, K.35, D.38, L.87, K.91 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.91 EDO.7: 4 residues within 4Å: Chain A: P.78, A.79, F.82, F.114 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.78 Water bridges: A:A.79, A:N.109, A:N.109 EDO.23: 3 residues within 4Å: Chain B: Q.36, Q.42 Ligands: DMS.17 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Q.36 EDO.32: 1 residues within 4Å: Chain B: E.331 1 PLIP interactions: 1 interactions with chain B Water bridges: B:T.328 EDO.34: 6 residues within 4Å: Chain C: E.31, L.34, K.35, D.38, L.87, K.91 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.38, C:K.91 EDO.40: 4 residues within 4Å: Chain C: P.78, A.79, F.82, F.114 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:P.78 Water bridges: C:A.79, C:N.109, C:N.109 EDO.56: 3 residues within 4Å: Chain D: Q.36, Q.42 Ligands: DMS.50 1 PLIP interactions: 1 interactions with chain D Water bridges: D:Q.36 EDO.65: 1 residues within 4Å: Chain D: E.331 2 PLIP interactions: 2 interactions with chain D Water bridges: D:T.328, D:E.331

32 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.2: 4 residues within 4Å: Chain A: E.5, N.147, I.148, A.149 Ligand excluded by PLIP DMS.3: 5 residues within 4Å: Chain A: N.12, R.15, E.16, G.17, V.224 Ligand excluded by PLIP DMS.4: 4 residues within 4Å: Chain A: A.59, D.60, I.153, Y.175 Ligand excluded by PLIP DMS.8: 4 residues within 4Å: Chain A: P.28, G.29, Q.32 Ligands: CL.5 Ligand excluded by PLIP DMS.9: 5 residues within 4Å: Chain A: I.30, L.34, Q.80, E.83, M.84 Ligand excluded by PLIP DMS.14: 10 residues within 4Å: Chain B: K.50, G.54, R.55, P.56 Chain D: P.56, T.57, Q.215 Ligands: CS.33, DMS.47, CS.66 Ligand excluded by PLIP DMS.15: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP DMS.16: 5 residues within 4Å: Chain B: Q.42, F.45, A.46, L.49, M.207 Ligand excluded by PLIP DMS.17: 6 residues within 4Å: Chain B: Q.36, K.37, D.38, P.39, Q.42 Ligands: EDO.23 Ligand excluded by PLIP DMS.18: 4 residues within 4Å: Chain B: P.56, E.211, A.214, Q.215 Ligand excluded by PLIP DMS.19: 4 residues within 4Å: Chain B: T.3, L.4, L.5, N.6 Ligand excluded by PLIP DMS.24: 5 residues within 4Å: Chain B: L.217, D.218, K.219, E.220, G.221 Ligand excluded by PLIP DMS.25: 4 residues within 4Å: Chain B: T.60, K.61 Chain D: D.47, N.51 Ligand excluded by PLIP DMS.26: 4 residues within 4Å: Chain B: H.357, K.360, M.361, E.364 Ligand excluded by PLIP DMS.27: 4 residues within 4Å: Chain B: I.262, G.265, H.267, H.273 Ligand excluded by PLIP DMS.28: 4 residues within 4Å: Chain B: R.70, E.367, K.368, E.369 Ligand excluded by PLIP DMS.35: 4 residues within 4Å: Chain C: E.5, N.147, I.148, A.149 Ligand excluded by PLIP DMS.36: 5 residues within 4Å: Chain C: N.12, R.15, E.16, G.17, V.224 Ligand excluded by PLIP DMS.37: 4 residues within 4Å: Chain C: A.59, D.60, I.153, Y.175 Ligand excluded by PLIP DMS.41: 4 residues within 4Å: Chain C: P.28, G.29, Q.32 Ligands: CL.38 Ligand excluded by PLIP DMS.42: 5 residues within 4Å: Chain C: I.30, L.34, Q.80, E.83, M.84 Ligand excluded by PLIP DMS.47: 10 residues within 4Å: Chain B: P.56, T.57, Q.215 Chain D: K.50, G.54, R.55, P.56 Ligands: DMS.14, CS.33, CS.66 Ligand excluded by PLIP DMS.48: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP DMS.49: 5 residues within 4Å: Chain D: Q.42, F.45, A.46, L.49, M.207 Ligand excluded by PLIP DMS.50: 6 residues within 4Å: Chain D: Q.36, K.37, D.38, P.39, Q.42 Ligands: EDO.56 Ligand excluded by PLIP DMS.51: 4 residues within 4Å: Chain D: P.56, E.211, A.214, Q.215 Ligand excluded by PLIP DMS.52: 4 residues within 4Å: Chain D: T.3, L.4, L.5, N.6 Ligand excluded by PLIP DMS.57: 5 residues within 4Å: Chain D: L.217, D.218, K.219, E.220, G.221 Ligand excluded by PLIP DMS.58: 4 residues within 4Å: Chain B: D.47, N.51 Chain D: T.60, K.61 Ligand excluded by PLIP DMS.59: 4 residues within 4Å: Chain D: H.357, K.360, M.361, E.364 Ligand excluded by PLIP DMS.60: 4 residues within 4Å: Chain D: I.262, G.265, H.267, H.273 Ligand excluded by PLIP DMS.61: 4 residues within 4Å: Chain D: R.70, E.367, K.368, E.369 Ligand excluded by PLIP

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

CL.5: 5 residues within 4Å: Chain A: G.29, I.30, E.31, Q.32 Ligands: DMS.8 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain A: H.92, P.93, T.94, I.95 Ligand excluded by PLIP CL.22: 4 residues within 4Å: Chain B: G.179, S.180, Y.181, E.182 Ligand excluded by PLIP CL.29: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.30: 1 residues within 4Å: Chain B: G.127 Ligand excluded by PLIP CL.31: 3 residues within 4Å: Chain B: D.225, S.249, G.251 Ligand excluded by PLIP CL.38: 5 residues within 4Å: Chain C: G.29, I.30, E.31, Q.32 Ligands: DMS.41 Ligand excluded by PLIP CL.43: 4 residues within 4Å: Chain C: H.92, P.93, T.94, I.95 Ligand excluded by PLIP CL.55: 4 residues within 4Å: Chain D: G.179, S.180, Y.181, E.182 Ligand excluded by PLIP CL.62: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.63: 1 residues within 4Å: Chain D: G.127 Ligand excluded by PLIP CL.64: 3 residues within 4Å: Chain D: D.225, S.249, G.251 Ligand excluded by PLIP

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

PEG.6: 7 residues within 4Å: Chain A: A.167, S.168, G.170, R.171, Y.203, H.204, A.206 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.203 PEG.39: 7 residues within 4Å: Chain C: A.167, S.168, G.170, R.171, Y.203, H.204, A.206 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.203

10 x CS: CESIUM ION(Non-covalent)

CS.11: 2 residues within 4Å: Chain A: F.107, G.110 No protein-ligand interaction detected (PLIP) CS.12: 3 residues within 4Å: Chain A: S.221, A.265, R.267 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:A.265 CS.20: 3 residues within 4Å: Chain B: T.66, T.69, T.71 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.71 CS.21: 6 residues within 4Å: Chain B: V.231, G.232, E.256, G.268, P.270, S.308 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:G.232 CS.33: 7 residues within 4Å: Chain B: G.54, P.56 Chain D: G.54, P.56 Ligands: DMS.14, DMS.47, CS.66 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Metal complexes: B:P.56, D:P.56 CS.44: 2 residues within 4Å: Chain C: F.107, G.110 No protein-ligand interaction detected (PLIP) CS.45: 3 residues within 4Å: Chain C: S.221, A.265, R.267 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:A.265 CS.53: 3 residues within 4Å: Chain D: T.66, T.69, T.71 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.71 CS.54: 6 residues within 4Å: Chain D: V.231, G.232, E.256, G.268, P.270, S.308 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:G.232 CS.66: 7 residues within 4Å: Chain B: G.54, P.56 Chain D: G.54, P.56 Ligands: DMS.14, CS.33, DMS.47 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Metal complexes: B:P.56, D:P.56

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

PLP.13: 17 residues within 4Å: Chain B: A.85, H.86, K.87, Q.114, T.190, C.230, V.231, G.232, G.233, G.234, S.235, N.236, G.303, A.348, E.350, S.377, G.378 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:A.85, B:K.87, B:A.348 Hydrogen bonds: B:G.232, B:G.233, B:G.234, B:S.235, B:N.236, B:N.236, B:S.377 Water bridges: B:T.190, B:T.190, B:S.235, B:S.235, B:A.237 Salt bridges: B:H.86, B:K.87 pi-Stacking: B:H.86 PLP.46: 17 residues within 4Å: Chain D: A.85, H.86, K.87, Q.114, T.190, C.230, V.231, G.232, G.233, G.234, S.235, N.236, G.303, A.348, E.350, S.377, G.378 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:A.85, D:K.87, D:A.348 Hydrogen bonds: D:T.190, D:G.232, D:G.233, D:G.234, D:S.235, D:N.236, D:N.236, D:S.377 Water bridges: D:S.235, D:S.235, D:A.237 Salt bridges: D:H.86, D:K.87 pi-Stacking: D:H.86

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hilario, E. et al., The internal aldimine form of the wild-type Salmonella Typhimurium Tryptophan Synthase in complex with cesium ion at the metal coordination site at 1.61 Angstrom resolution. To be Published

Release Date

2022-03-02

Peptides

Tryptophan synthase alpha chain: AC
Tryptophan synthase beta chain: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

Tryptophan synthase alpha chain

Tryptophan synthase beta chain

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