SMTL ID : 7m3s.1 (1 other biounit)

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 1.55 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

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

hetero-1-1-mer

Ligands

2 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, I.64, L.100, L.127, A.129, I.153, Y.175, T.183, G.184, F.212, G.213, G.234, S.235 Chain B: P.18 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.100, 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 F6F.7: 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, T.190, G.193, P.194, F.280, G.281, F.306 Ligands: PLP.4 19 PLIP interactions: 19 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:G.111, B:A.112, B:G.113, B:Q.114, B:H.115, B:G.116 Water bridges: B:K.87, B:T.190, B:A.302, B:G.303, B:G.303 Salt bridges: B:K.87 Halogen bonds: B:Y.186

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

EDO.2: 4 residues within 4Å: Chain A: N.108, N.109 Chain B: R.275, A.290 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.275, A:N.108 EDO.5: 4 residues within 4Å: Chain B: T.3, L.4, L.5, N.6 No protein-ligand interaction detected (PLIP) EDO.8: 4 residues within 4Å: Chain B: T.248, S.249, V.250, G.251 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.321 Water bridges: B:D.225, B:G.251, B:R.321, B:D.323 EDO.9: 4 residues within 4Å: Chain B: E.334, K.337, T.338, R.341 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.334, B:E.334, B:R.341 EDO.11: 3 residues within 4Å: Chain B: K.272, H.273, G.274 1 PLIP interactions: 1 interactions with chain B Water bridges: B:G.274 EDO.12: 3 residues within 4Å: Chain B: Q.42, F.45, A.46 No protein-ligand interaction detected (PLIP) EDO.13: 2 residues within 4Å: Chain B: E.182, T.183 No protein-ligand interaction detected (PLIP)

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

CL.3: 2 residues within 4Å: Chain A: A.113, F.114 Ligand excluded by PLIP CL.16: 0 residues within 4Å: (No contacts) 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.7 18 PLIP interactions: 18 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 pi-Stacking: B:H.86

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

PEG.6: 2 residues within 4Å: Chain B: A.214, Q.215 2 PLIP interactions: 2 interactions with chain B Water bridges: B:Q.215, B:D.218

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

DMS.10: 2 residues within 4Å: Chain B: F.385, H.388 1 PLIP interactions: 1 interactions with chain B pi-Cation interactions: B:H.388

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

NA.14: 4 residues within 4Å: Chain B: G.232, P.270, F.306, S.308 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.308, B:S.308 NA.15: 3 residues within 4Å: Chain B: E.296, S.297, D.305 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.296, 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 1.55 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

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

Related Entries With Identical Sequence