SMTL ID : 7ly8.1

The internal aldimine form of the wild-type Salmonella Typhimurium Tryptophan Synthase in complex with two molecules of N-(4'-trifluoromethoxybenzoyl)-2-amino-1-ethylphosphate (F6F) inhibitor at the enzyme alpha-site, a single F6F molecule at the enzyme beta-site, and sodium ion at the metal coordination site at 1.55 Angstrom resolution. One 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 1.55 Å

Oligo State

hetero-1-1-mer

Ligands

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

F6F.1: 17 residues within 4Å: Chain A: F.22, E.49, A.59, D.60, L.100, L.127, A.129, I.153, Y.175, F.212, G.213, I.232, S.233, G.234, S.235 Chain B: P.18 Ligands: F6F.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.100, A:Y.175 Hydrogen bonds: A:Y.175, A:F.212, A:G.213, A:G.234, A:S.235 Water bridges: A:I.214, A:I.214, A:S.235, A:S.235 pi-Stacking: A:F.212 F6F.2: 14 residues within 4Å: Chain A: L.58, A.59, D.60, G.61, I.64, F.212, S.235 Chain B: P.18, I.20, L.21, L.174, R.175, S.178 Ligands: F6F.1 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:A.59, A:F.212, B:P.18, B:I.20 Hydrogen bonds: A:D.60, A:G.61, B:S.178 Water bridges: A:I.64 Halogen bonds: A:L.58 F6F.5: 19 residues within 4Å: Chain B: K.87, E.109, T.110, G.111, A.112, G.113, Q.114, H.115, C.170, L.174, Y.186, L.188, G.189, T.190, G.193, P.194, F.280, F.306 Ligands: PLP.4 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:E.109, B:L.188, B:T.190, B:F.306, B:F.306 Hydrogen bonds: B:E.109, 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

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

CL.3: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.12: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.13: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.14: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain B: E.220, G.221 Ligand excluded by PLIP

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

PLP.4: 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, B:E.350 Hydrogen bonds: B:K.87, 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.6: 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

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

EDO.7: 3 residues within 4Å: Chain B: T.3, L.5, N.6 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.3 Water bridges: B:N.6 EDO.8: 1 residues within 4Å: Chain B: L.4 No protein-ligand interaction detected (PLIP) EDO.9: 4 residues within 4Å: Chain B: Y.8, G.10, E.11, K.283 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.10, B:K.283 EDO.10: 3 residues within 4Å: Chain B: L.271, K.272, N.317 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.317

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

NA.11: 4 residues within 4Å: Chain B: G.232, P.270, F.306, S.308 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.308

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 two molecules of N-(4'-trifluoromethoxybenzoyl)-2-amino-1-ethylphosphate (F6F) inhibitor at the enzyme alpha-site, a single F6F molecule at the enzyme beta-site, and sodium ion at the metal coordination site at 1.55 Angstrom resolution. One of the beta-Q114 rotamer conformations allows a hydrogen bond to form with the PLP oxygen at the position 3 in the ring. To be Published

Release Date

2022-03-09

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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