SMTL ID : 7kxc.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, sodium ion at the metal coordination site and benzimidazole (BZI) at the enzyme beta-site at 1.30 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 1.51 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

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

EDO.2: 5 residues within 4Å: Chain A: L.144, N.147, I.148, A.149, R.171 3 PLIP interactions: 3 interactions with chain A Water bridges: A:L.144, A:N.147, A:A.149 EDO.3: 5 residues within 4Å: Chain A: A.190, L.191, P.192, L.193, H.194 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.191 EDO.9: 3 residues within 4Å: Chain B: I.319, G.320, R.321 No protein-ligand interaction detected (PLIP) EDO.10: 7 residues within 4Å: Chain B: K.213, A.242, D.243, F.244, I.245, N.246, D.247 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.213, B:I.245, B:N.246, B:D.247 Water bridges: B:R.206, B:A.242 EDO.11: 2 residues within 4Å: Chain B: Y.8, G.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.10

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

CL.4: 4 residues within 4Å: Chain A: S.247, P.248, K.249, Q.250 Ligand excluded by PLIP

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

0JO.5: 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.6 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:A.85, B:L.166, B:A.348, B:E.350 Hydrogen bonds: 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.6: 11 residues within 4Å: Chain B: K.87, E.109, L.166, C.170, G.189, T.190, G.232, G.233, G.303, F.306 Ligands: 0JO.5 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.166, B:L.166, B:T.190, B:F.306 Hydrogen bonds: B:K.87, B:K.87 pi-Stacking: B:F.306 BZI.7: 4 residues within 4Å: Chain B: T.3, L.4, L.5, N.6 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.3 Water bridges: B:T.3, B:T.3

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

PEG.8: 3 residues within 4Å: Chain B: E.211, A.214, Q.215 3 PLIP interactions: 3 interactions with chain B Water bridges: B:E.210, B:Q.215, B:D.218

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

PGE.12: 5 residues within 4Å: Chain B: D.47, L.48, N.51, Y.52, L.125 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.51

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

NA.13: 5 residues within 4Å: Chain B: G.232, G.268, 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 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, sodium ion at the metal coordination site and benzimidazole (BZI) at the enzyme beta-site at 1.30 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

2021-12-15

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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