SMTL ID : 7kqf.1

The internal aldimine form of the wild-type Tryptophan Synthase from Salmonella in complex with inhibitor N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the enzyme alpha-site and cesium ion at the metal coordination site at 1.47 Angstrom resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.47 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 13 PLIP interactions: 13 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 pi-Stacking: A:F.212

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

EDO.2: 6 residues within 4Å: Chain A: A.167, S.168, G.170, R.171, H.204, A.206 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.170, A:A.206 Water bridges: A:A.167, A:G.170, A:R.171 EDO.4: 3 residues within 4Å: Chain A: F.82, N.109, F.114 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.113 Water bridges: A:N.108, A:N.109 EDO.14: 3 residues within 4Å: Chain B: A.43, Q.44, D.47 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Q.44 EDO.16: 9 residues within 4Å: Chain B: K.87, T.110, G.111, A.112, G.113, Q.114, H.115, G.303 Ligands: PLP.11 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:K.87, B:T.110, B:G.111, B:A.112, B:G.113, B:Q.114, B:H.115 Water bridges: B:E.109, B:A.112

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

PEG.3: 5 residues within 4Å: Chain A: R.164, Q.165, S.168, Y.169 Ligands: CL.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.168 PEG.5: 6 residues within 4Å: Chain A: S.215, P.217, S.257, F.258, A.261 Ligands: CL.9 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.215 PEG.7: 9 residues within 4Å: Chain A: F.107, I.111, E.135, P.138, F.139 Chain B: Y.8, Y.16, I.278, K.283 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:E.135, B:Y.16, B:K.283 Water bridges: B:Y.8, B:Y.8 PEG.12: 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 PEG.13: 4 residues within 4Å: Chain B: T.3, L.4, L.5, N.6 1 PLIP interactions: 1 interactions with chain B Water bridges: B:T.3 PEG.15: 7 residues within 4Å: Chain B: N.64, I.65, T.66, A.67, T.69, M.362 Ligands: CL.23 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.363

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

DMS.6: 7 residues within 4Å: Chain A: M.1, E.5, L.144, N.147, I.148, A.149, R.171 3 PLIP interactions: 3 interactions with chain A Water bridges: A:M.1, A:A.149 Salt bridges: A:E.5

4 x CS: CESIUM ION(Non-covalent)

CS.8: 3 residues within 4Å: Chain A: S.221, A.265, R.267 No protein-ligand interaction detected (PLIP) CS.17: 2 residues within 4Å: Chain B: D.225, S.249 No protein-ligand interaction detected (PLIP) CS.18: 3 residues within 4Å: Chain B: T.66, T.69, T.71 No protein-ligand interaction detected (PLIP) CS.19: 6 residues within 4Å: Chain B: V.231, G.232, E.256, G.268, P.270, S.308 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:G.232

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

CL.9: 1 residues within 4Å: Ligands: PEG.5 Ligand excluded by PLIP CL.10: 1 residues within 4Å: Ligands: PEG.3 Ligand excluded by PLIP CL.20: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.21: 1 residues within 4Å: Chain B: G.274 Ligand excluded by PLIP CL.22: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.23: 2 residues within 4Å: Chain B: A.67 Ligands: PEG.15 Ligand excluded by PLIP

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

PLP.11: 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: EDO.16 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:A.85, B:K.87, B:A.348 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:S.235, B:S.235, B:A.237 Salt bridges: B:H.86, B:K.87 pi-Stacking: B:H.86

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hilario, E. et al., The internal aldimine form of the wild-type Tryptophan Synthase from Salmonella in complex with inhibitor N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the enzyme alpha-site and cesium ion at the metal coordination site at 1.47 Angstrom resolution. To be Published

Release Date

2021-11-24

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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