SMTL ID : 7lvx.1

The internal aldimine form of the wild-type Salmonella Typhimurium Tryptophan Synthase in complex with N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the enzyme alpha-site and cesium ion at the metal coordination site at 1.55 Angstrom resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

hetero-1-1-mer

Ligands

1 x F9F: 2-({[4-(TRIFLUOROMETHOXY)PHENYL]SULFONYL}AMINO)ETHYL DIHYDROGEN PHOSPHATE(Non-covalent)

F9F.1: 18 residues within 4Å: Chain A: F.22, E.49, A.59, I.64, L.100, L.127, A.129, I.153, Y.175, T.183, G.184, F.212, G.213, I.232, S.233, G.234, S.235 Chain B: P.18 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.100, A:L.127, A:I.153, A:Y.175, A:T.183 Hydrogen bonds: A:Y.175, A:G.184, A:F.212, A:G.213, A:G.234, A:S.235 Water bridges: A:I.214, A:I.214, A:A.236 pi-Stacking: A:F.212

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

EDO.2: 6 residues within 4Å: Chain A: V.133, E.134, S.136, A.137, R.140, Y.169 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.136, A:S.136, A:A.137, A:R.140, A:R.140 EDO.3: 1 residues within 4Å: Chain A: A.246 No protein-ligand interaction detected (PLIP) EDO.4: 6 residues within 4Å: Chain A: M.1, E.5, N.147, A.149, G.172 Ligands: CL.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.5, A:N.147 EDO.14: 5 residues within 4Å: Chain B: I.65, T.338, H.342, M.362, R.363 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.65, B:H.342, B:R.363

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

CL.5: 4 residues within 4Å: Chain A: H.92, P.93, T.94, I.95 Ligand excluded by PLIP CL.6: 5 residues within 4Å: Chain A: E.2, R.3, Y.4, E.5 Ligands: EDO.4 Ligand excluded by PLIP CL.7: 1 residues within 4Å: Chain A: F.114 Ligand excluded by PLIP CL.18: 1 residues within 4Å: Chain B: Y.8 Ligand excluded by PLIP CL.19: 4 residues within 4Å: Chain B: T.3, L.4, L.5, N.6 Ligand excluded by PLIP CL.20: 1 residues within 4Å: Chain B: F.385 Ligand excluded by PLIP CL.21: 1 residues within 4Å: Chain B: D.218 Ligand excluded by PLIP CL.22: 2 residues within 4Å: Chain B: D.225, S.249 Ligand excluded by PLIP

6 x CS: CESIUM ION(Non-covalent)

CS.8: 3 residues within 4Å: Chain A: S.221, A.265, R.267 No protein-ligand interaction detected (PLIP) CS.9: 3 residues within 4Å: Chain A: A.167, G.170, H.204 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:A.167, H2O.7 CS.10: 3 residues within 4Å: Chain A: F.107, N.108, G.110 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:F.107, H2O.9, H2O.12 CS.12: 3 residues within 4Å: Chain B: T.66, T.69, T.71 No protein-ligand interaction detected (PLIP) CS.13: 6 residues within 4Å: Chain B: V.231, G.232, E.256, G.268, P.270, S.308 No protein-ligand interaction detected (PLIP) CS.23: 2 residues within 4Å: Chain B: G.54, P.56 No protein-ligand interaction detected (PLIP)

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

PLP.11: 18 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, L.304, 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

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

DMS.15: 2 residues within 4Å: Chain B: L.271, N.317 No protein-ligand interaction detected (PLIP) DMS.16: 5 residues within 4Å: Chain B: Q.36, K.37, D.38, P.39, Q.42 No protein-ligand interaction detected (PLIP) DMS.17: 5 residues within 4Å: Chain B: Q.42, F.45, A.46, L.49, M.207 No protein-ligand interaction detected (PLIP)

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 N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the enzyme alpha-site and cesium ion at the metal coordination site at 1.55 Angstrom resolution. To be Published

Release Date

2022-03-02

Peptides

Tryptophan synthase alpha chain: A
Tryptophan synthase beta chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Tryptophan synthase alpha chain

Tryptophan synthase beta chain

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