SMTL ID : 7lv5.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 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 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.100, A:L.127, 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

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

DMS.2: 3 residues within 4Å: Chain A: A.113, F.114, R.117 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.109

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

PEG.3: 5 residues within 4Å: Chain A: S.215, P.217, S.257, F.258, A.261 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.215 Water bridges: A:E.254, A:F.258 PEG.13: 3 residues within 4Å: Chain B: E.211, A.214, Q.215 1 PLIP interactions: 1 interactions with chain B Water bridges: B:D.218

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: S.247, P.248, K.249, Q.250 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.249, A:K.249, A:K.249, A:Q.250

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

EDO.5: 4 residues within 4Å: Chain A: M.1, N.147, A.149, R.171 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.1 EDO.11: 4 residues within 4Å: Chain B: T.3, L.4, L.5, N.6 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.4 EDO.12: 4 residues within 4Å: Chain B: D.218, K.219, E.220, G.221 3 PLIP interactions: 3 interactions with chain B Water bridges: B:L.217, B:D.218, B:D.218 EDO.14: 4 residues within 4Å: Chain B: T.289, A.290, D.291, Q.293 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.289, B:A.290, B:D.291, B:D.291 Water bridges: B:D.291, B:D.291 EDO.16: 5 residues within 4Å: Chain B: G.259, H.260, T.328, D.329, D.330 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.259, B:D.329, B:D.330 Water bridges: B:H.260

4 x CS: CESIUM ION(Non-covalent)

CS.6: 3 residues within 4Å: Chain A: S.221, A.265, R.267 No protein-ligand interaction detected (PLIP) CS.8: 3 residues within 4Å: Chain B: T.66, T.69, T.71 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:T.71, H2O.24 CS.9: 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.17: 2 residues within 4Å: Chain B: G.54, P.56 No protein-ligand interaction detected (PLIP)

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

PLP.7: 19 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 Ligands: HIS.15 19 PLIP interactions: 18 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:A.85, B:K.87, B:A.348, H.15 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

1 x BCN: BICINE(Non-covalent)

BCN.10: 9 residues within 4Å: Chain B: T.248, S.249, V.250, G.251, L.252, G.320, R.321, A.322, D.323 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.249, B:L.252, B:L.252, B:R.321, B:R.321 Salt bridges: B:R.321, B:D.323

1 x HIS: HISTIDINE(Non-covalent)

HIS.15: 12 residues within 4Å: Chain B: K.87, E.109, T.110, G.111, A.112, G.113, Q.114, H.115, L.166, G.189, F.306 Ligands: PLP.7 10 PLIP interactions: 9 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: B:T.110, B:G.111, B:A.112, B:G.113, B:Q.114, B:H.115 Water bridges: B:E.109, B:T.190 Salt bridges: B:K.87, H.15

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

CL.18: 0 residues within 4Å: (No contacts) Ligand excluded by 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 inhibitor N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the enzyme alpha-site, cesium ion at the metal coordination site and L-Histidine at the enzyme beta-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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