SMTL ID : 7kyt.1

The aminoacrylate 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 benzimidazole (BZI) at the enzyme beta-site at 1.35 Angstrom resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.35 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 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: 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 pi-Stacking: A:F.212

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

EDO.2: 2 residues within 4Å: Chain A: S.168, Y.169 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.168 EDO.3: 5 residues within 4Å: Chain A: E.134, E.135 Chain B: P.7, Y.8 Ligands: BZI.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.134 EDO.10: 2 residues within 4Å: Chain B: E.263, T.264 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.263 Water bridges: B:H.260 EDO.11: 3 residues within 4Å: Chain B: G.265, M.287, E.295 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.295 Water bridges: B:T.264 EDO.12: 3 residues within 4Å: Chain B: A.136, K.137, A.164 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.136 Water bridges: B:S.163 EDO.13: 2 residues within 4Å: Chain B: I.262, E.263 1 PLIP interactions: 1 interactions with chain B Water bridges: B:E.263

2 x CS: CESIUM ION(Non-covalent)

CS.4: 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.5: 6 residues within 4Å: Chain B: V.231, G.232, G.268, L.304, F.306, S.308 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:G.232, B:F.306, H2O.18

1 x 0JO: 2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid(Non-covalent)

0JO.6: 25 residues within 4Å: Chain B: A.85, H.86, K.87, T.110, G.111, A.112, G.113, Q.114, H.115, L.166, 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: BZI.7 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:A.85, B:L.166, B:A.348, B:E.350 Hydrogen bonds: B:K.87, B:T.110, B:G.111, B:A.112, B:G.113, B:Q.114, B:H.115, B:G.232, B:G.233, B:G.234, B:S.235, B:S.235, B:N.236, B:N.236, B:S.377 Water bridges: B:A.237 Salt bridges: B:H.86, B:K.87, B:K.87 pi-Stacking: B:H.86

2 x BZI: BENZIMIDAZOLE(Non-covalent)

BZI.7: 10 residues within 4Å: Chain B: K.87, E.109, L.166, C.170, G.189, T.190, G.232, G.233, F.306 Ligands: 0JO.6 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.166, B:T.190 Hydrogen bonds: B:K.87, B:K.87, B:G.189 pi-Stacking: B:F.306 BZI.9: 6 residues within 4Å: Chain B: T.3, L.4, L.5, N.6, P.7 Ligands: EDO.3 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:N.6 Hydrogen bonds: B:T.3

1 x BCN: BICINE(Non-covalent)

BCN.8: 5 residues within 4Å: Chain A: T.77 Chain B: T.289, A.290, D.291, Q.293 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.291, B:D.291 Water bridges: B:A.290, B:A.290, B:D.291 Salt bridges: B:D.291

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hilario, E. et al., The aminoacrylate 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 benzimidazole (BZI) at the enzyme beta-site at 1.35 Angstrom resolution. To be Published

Release Date

2021-12-22

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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