SMTL ID : 7m2l.1

The internal aldimine form of the wild-type Salmonella Typhimurium Tryptophan Synthase in complex with N-(4'-trifluoromethoxybenzoyl)-2-amino-1-ethylphosphate (F6F) inhibitor at the alpha-and beta-site, sodium ion at the metal coordination site, and another F6F molecule at the enzyme beta-site at 1.60 Angstrom resolution. Two of the beta-Q114 rotamer conformations allows a hydrogen bond to form with the PLP oxygen at the position 3 in the ring

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

hetero-1-1-mer

Ligands

2 x F6F: 2-{[4-(TRIFLUOROMETHOXY)BENZOYL]AMINO}ETHYL DIHYDROGEN PHOSPHATE(Non-covalent)

F6F.1: 18 residues within 4Å: Chain A: F.22, E.49, A.59, D.60, I.64, L.100, L.127, A.129, I.153, Y.175, T.183, G.184, F.212, G.213, S.233, G.234, S.235 Chain B: P.18 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.100, 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:F.212, A:I.214 pi-Stacking: A:F.212 F6F.5: 20 residues within 4Å: Chain B: K.87, E.109, T.110, G.111, A.112, G.113, Q.114, H.115, L.166, C.170, L.174, Y.186, L.188, G.189, T.190, G.193, P.194, F.280, F.306 Ligands: PLP.7 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:E.109, B:L.188, B:T.190, B:F.306 Hydrogen bonds: B:E.109, B:T.110, B:T.110, B:G.111, B:A.112, B:G.113, B:Q.114, B:H.115, B:G.116 Water bridges: B:T.190 Salt bridges: B:K.87 Halogen bonds: B:Y.186

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

EDO.2: 3 residues within 4Å: Chain A: F.82, A.113, F.114 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.113 Water bridges: A:P.78, A:A.79, A:N.108 EDO.4: 3 residues within 4Å: Chain B: T.3, L.4, L.5 1 PLIP interactions: 1 interactions with chain B Water bridges: B:T.3 EDO.9: 5 residues within 4Å: Chain B: L.59, T.60, K.61, Y.74, K.219 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.59, B:K.61 Water bridges: B:K.61, B:K.61 EDO.10: 2 residues within 4Å: Chain B: F.385, H.388 No protein-ligand interaction detected (PLIP)

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

CL.3: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.13: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.14: 1 residues within 4Å: Chain B: K.272 Ligand excluded by PLIP CL.15: 1 residues within 4Å: Chain B: Q.42 Ligand excluded by PLIP CL.16: 1 residues within 4Å: Chain B: E.182 Ligand excluded by PLIP

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.6: 5 residues within 4Å: Chain B: E.210, E.211, A.214, Q.215, D.218 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.210 Water bridges: B:Q.215, B:D.218

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: F6F.5 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:A.85, B:K.87, B:A.348 Hydrogen bonds: B:K.87, B:Q.114, B:T.190, 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:A.237 Salt bridges: B:H.86, B:K.87 pi-Stacking: B:H.86

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

PEG.8: 2 residues within 4Å: Chain B: R.363, E.364 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.364 Water bridges: B:R.363, B:E.364

2 x NA: SODIUM ION(Non-functional Binders)

NA.11: 4 residues within 4Å: Chain B: G.232, P.270, F.306, S.308 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.232, B:S.308 Water bridges: B:F.306 NA.12: 3 residues within 4Å: Chain B: E.296, S.297, D.305 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.296, B:S.297, B:S.297 Water bridges: B:T.165

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'-trifluoromethoxybenzoyl)-2-amino-1-ethylphosphate (F6F) inhibitor at the alpha-and beta-site, sodium ion at the metal coordination site, and another F6F molecule at the enzyme beta-site at 1.60 Angstrom resolution. To be Published

Release Date

2021-09-22

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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