SMTL ID : 7lgx.1

The aminoacrylate form of mutant beta-K167T Salmonella typhimurium Tryptophan Synthase in complex with with inhibitor N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the enzyme alpha-site, benzimidazole (BZI) at the enzyme beta site and cesium ion at the metal coordination site at 1.80 Angstrom resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-2-2-mer

Ligands

2 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, 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 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:A.59, A:L.100, A:L.100, A:Y.175, A:T.183 Hydrogen bonds: A:G.184, A:G.213, A:G.234, A:S.235 pi-Stacking: A:F.212 F9F.19: 18 residues within 4Å: Chain C: 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 D: P.18 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:A.59, C:L.100, C:L.100, C:Y.175, C:T.183 Hydrogen bonds: C:Y.175, C:G.184, C:G.213, C:G.234, C:S.235 pi-Stacking: C:F.212

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

EDO.2: 3 residues within 4Å: Chain A: A.113, F.114, R.117 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.113 Water bridges: A:L.105, A:R.117 EDO.7: 4 residues within 4Å: Chain B: D.218, K.219, E.220, G.221 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.218 EDO.10: 6 residues within 4Å: Chain B: H.273, G.274, R.275, M.286, M.287, Q.288 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.288 Water bridges: B:H.273 EDO.11: 4 residues within 4Å: Chain B: I.262, E.263, G.265, H.267 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.263 Water bridges: B:H.273 EDO.13: 3 residues within 4Å: Chain B: H.260, G.261, E.263 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.263 EDO.20: 3 residues within 4Å: Chain C: A.113, F.114, R.117 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:A.113 Water bridges: C:L.105, C:R.117 EDO.25: 4 residues within 4Å: Chain D: D.218, K.219, E.220, G.221 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.218 EDO.28: 6 residues within 4Å: Chain D: H.273, G.274, R.275, M.286, M.287, Q.288 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.288 Water bridges: D:H.273 EDO.29: 4 residues within 4Å: Chain D: I.262, E.263, G.265, H.267 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.263 Water bridges: D:H.273 EDO.31: 3 residues within 4Å: Chain D: H.260, G.261, E.263 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.263

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

CL.3: 3 residues within 4Å: Chain A: A.167, G.170, H.204 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain B: Q.42, F.45 Ligand excluded by PLIP CL.17: 3 residues within 4Å: Chain B: S.143 Chain D: I.384, F.385 Ligand excluded by PLIP CL.18: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.21: 3 residues within 4Å: Chain C: A.167, G.170, H.204 Ligand excluded by PLIP CL.34: 2 residues within 4Å: Chain D: Q.42, F.45 Ligand excluded by PLIP CL.35: 3 residues within 4Å: Chain B: I.384, F.385 Chain D: S.143 Ligand excluded by PLIP CL.36: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

4 x BZI: BENZIMIDAZOLE(Non-covalent)

BZI.4: 10 residues within 4Å: Chain B: K.87, E.109, H.115, L.166, G.189, T.190, G.232, G.233, F.306 Ligands: 0JO.6 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.166, B:T.190, B:F.306 Hydrogen bonds: B:K.87, B:K.87, B:E.109 pi-Stacking: B:F.306 BZI.5: 5 residues within 4Å: Chain B: T.3, L.4, L.5, N.6, P.7 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:N.6 Water bridges: B:T.3, B:N.6 BZI.22: 10 residues within 4Å: Chain D: K.87, E.109, H.115, L.166, G.189, T.190, G.232, G.233, F.306 Ligands: 0JO.24 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:L.166, D:T.190, D:F.306 Hydrogen bonds: D:K.87, D:K.87 pi-Stacking: D:F.306 BZI.23: 5 residues within 4Å: Chain D: T.3, L.4, L.5, N.6, P.7 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:N.6 Water bridges: D:T.3, D:N.6

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

0JO.6: 24 residues within 4Å: Chain B: A.85, H.86, K.87, T.110, G.111, A.112, G.113, Q.114, H.115, 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.4 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:A.85, B:A.348, B:E.350 Hydrogen bonds: B:K.87, B:G.111, B:A.112, B:G.113, B:Q.114, B:H.115, B:T.190, B:T.190, 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 0JO.24: 24 residues within 4Å: Chain D: A.85, H.86, K.87, T.110, G.111, A.112, G.113, Q.114, H.115, 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.22 25 PLIP interactions: 25 interactions with chain D Hydrophobic interactions: D:A.85, D:A.348, D:E.350 Hydrogen bonds: D:K.87, D:T.110, D:G.111, D:A.112, D:G.113, D:Q.114, D:H.115, D:T.190, D:T.190, D:G.232, D:G.233, D:G.234, D:S.235, D:S.235, D:N.236, D:N.236, D:S.377 Water bridges: D:A.237 Salt bridges: D:H.86, D:K.87, D:K.87 pi-Stacking: D:H.86

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

DMS.8: 9 residues within 4Å: Chain B: K.50, G.54, R.55, P.56 Chain D: P.56, T.57, A.58, Q.215 Ligands: DMS.26 No protein-ligand interaction detected (PLIP) DMS.9: 2 residues within 4Å: Chain B: R.363, E.364 No protein-ligand interaction detected (PLIP) DMS.26: 9 residues within 4Å: Chain B: P.56, T.57, A.58, Q.215 Chain D: K.50, G.54, R.55, P.56 Ligands: DMS.8 No protein-ligand interaction detected (PLIP) DMS.27: 2 residues within 4Å: Chain D: R.363, E.364 No protein-ligand interaction detected (PLIP)

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

PEG.12: 6 residues within 4Å: Chain B: N.6, Y.8, F.9, Q.312, Y.315, L.316 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.8, B:Q.312 Water bridges: B:G.10 PEG.30: 6 residues within 4Å: Chain D: N.6, Y.8, F.9, Q.312, Y.315, L.316 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Y.8, D:Q.312 Water bridges: D:G.10

4 x CS: CESIUM ION(Non-covalent)

CS.14: 3 residues within 4Å: Chain B: T.66, T.69, T.71 No protein-ligand interaction detected (PLIP) CS.15: 6 residues within 4Å: Chain B: V.231, G.232, G.268, L.304, F.306, S.308 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:G.232, B:F.306 CS.32: 3 residues within 4Å: Chain D: T.66, T.69, T.71 No protein-ligand interaction detected (PLIP) CS.33: 6 residues within 4Å: Chain D: V.231, G.232, G.268, L.304, F.306, S.308 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:G.232, D:F.306

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hilario, E. et al., The aminoacrylate form of mutant beta-K167T Salmonella typhimurium Tryptophan Synthase in complex with with inhibitor N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the enzyme alpha-site, benzimidazole (BZI) at the enzyme beta site and cesium ion at the metal coordination site at 1.80 Angstrom resolution. To be Published

Release Date

2022-01-26

Peptides

Tryptophan synthase alpha chain: AC
Tryptophan synthase beta chain: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

Tryptophan synthase alpha chain

Tryptophan synthase beta chain

Related Entries With Identical Sequence