SMTL ID : 7lkl.1

The internal aldimine 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, cesium ion at the metal coordination site and the product L-tryptophan at the enzyme beta-site at 1.05 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 1.05 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, 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 F9F.39: 18 residues within 4Å: Chain C: 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 D: P.18 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:L.100, C:L.127, C:Y.175, C:T.183 Hydrogen bonds: C:G.184, C:F.212, C:G.213, C:G.234, C:S.235 Water bridges: C:I.214, C:I.214, C:A.236 pi-Stacking: C:F.212

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

DMS.2: 5 residues within 4Å: Chain A: I.41, H.92, P.93, T.94, I.95 Ligand excluded by PLIP DMS.4: 5 residues within 4Å: Chain A: N.12, R.15, E.16, G.17, V.224 Ligand excluded by PLIP DMS.5: 7 residues within 4Å: Chain A: L.191, P.192, L.193, Q.210, A.222, A.223, A.226 Ligand excluded by PLIP DMS.6: 4 residues within 4Å: Chain A: S.55, L.69, F.72 Chain B: G.162 Ligand excluded by PLIP DMS.7: 8 residues within 4Å: Chain A: M.1, R.3, E.119, V.123, D.124, H.146, N.147, I.148 Ligand excluded by PLIP DMS.9: 8 residues within 4Å: Chain A: V.128, V.131, S.136, F.139, R.140, P.150, I.151, F.152 Ligand excluded by PLIP DMS.14: 5 residues within 4Å: Chain B: P.56, T.57, A.58, Q.215 Ligands: EDO.29 Ligand excluded by PLIP DMS.15: 7 residues within 4Å: Chain A: S.180 Chain B: S.178, G.179, S.180, Y.181, E.182 Ligands: TRP.3 Ligand excluded by PLIP DMS.16: 5 residues within 4Å: Chain B: Q.42, F.45, A.46, L.49, M.207 Ligand excluded by PLIP DMS.20: 4 residues within 4Å: Chain B: Y.133, E.172, R.175, D.176 Ligand excluded by PLIP DMS.22: 4 residues within 4Å: Chain B: T.3, L.4, L.5, N.6 Ligand excluded by PLIP DMS.26: 5 residues within 4Å: Chain B: I.65, T.66, A.67, T.69, M.362 Ligand excluded by PLIP DMS.27: 5 residues within 4Å: Chain B: R.141, T.165, E.296, S.297, D.305 Ligand excluded by PLIP DMS.40: 5 residues within 4Å: Chain C: I.41, H.92, P.93, T.94, I.95 Ligand excluded by PLIP DMS.42: 5 residues within 4Å: Chain C: N.12, R.15, E.16, G.17, V.224 Ligand excluded by PLIP DMS.43: 7 residues within 4Å: Chain C: L.191, P.192, L.193, Q.210, A.222, A.223, A.226 Ligand excluded by PLIP DMS.44: 4 residues within 4Å: Chain C: S.55, L.69, F.72 Chain D: G.162 Ligand excluded by PLIP DMS.45: 8 residues within 4Å: Chain C: M.1, R.3, E.119, V.123, D.124, H.146, N.147, I.148 Ligand excluded by PLIP DMS.47: 8 residues within 4Å: Chain C: V.128, V.131, S.136, F.139, R.140, P.150, I.151, F.152 Ligand excluded by PLIP DMS.52: 5 residues within 4Å: Chain D: P.56, T.57, A.58, Q.215 Ligands: EDO.67 Ligand excluded by PLIP DMS.53: 7 residues within 4Å: Chain C: S.180 Chain D: S.178, G.179, S.180, Y.181, E.182 Ligands: TRP.41 Ligand excluded by PLIP DMS.54: 5 residues within 4Å: Chain D: Q.42, F.45, A.46, L.49, M.207 Ligand excluded by PLIP DMS.58: 4 residues within 4Å: Chain D: Y.133, E.172, R.175, D.176 Ligand excluded by PLIP DMS.60: 4 residues within 4Å: Chain D: T.3, L.4, L.5, N.6 Ligand excluded by PLIP DMS.64: 5 residues within 4Å: Chain D: I.65, T.66, A.67, T.69, M.362 Ligand excluded by PLIP DMS.65: 5 residues within 4Å: Chain D: R.141, T.165, E.296, S.297, D.305 Ligand excluded by PLIP

4 x TRP: TRYPTOPHAN(Non-covalent)

TRP.3: 8 residues within 4Å: Chain A: P.156, N.157, R.179, S.180 Chain B: I.20, Y.181, E.182 Ligands: DMS.15 8 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: B:I.20, A:P.156, A:P.156, A:N.157 Hydrogen bonds: B:E.182, A:S.180, W.3, W.3 TRP.13: 15 residues within 4Å: Chain B: K.87, E.109, T.110, G.111, A.112, G.113, Q.114, H.115, L.166, T.190, G.233, A.302, G.303, F.306 Ligands: PLP.32 13 PLIP interactions: 13 interactions with chain B, Hydrophobic interactions: B:L.166, 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:A.302 Salt bridges: B:K.87 TRP.41: 8 residues within 4Å: Chain C: P.156, N.157, R.179, S.180 Chain D: I.20, Y.181, E.182 Ligands: DMS.53 8 PLIP interactions: 4 interactions with chain C, 2 Ligand-Ligand interactions, 2 interactions with chain D Hydrophobic interactions: C:P.156, C:P.156, C:N.157, D:I.20 Hydrogen bonds: C:S.180, W.41, W.41, D:E.182 TRP.51: 15 residues within 4Å: Chain D: K.87, E.109, T.110, G.111, A.112, G.113, Q.114, H.115, L.166, T.190, G.233, A.302, G.303, F.306 Ligands: PLP.70 13 PLIP interactions: 13 interactions with chain D, Hydrophobic interactions: D:L.166, D:T.190, D:F.306, D:F.306 Hydrogen bonds: D:E.109, D:E.109, D:G.111, D:A.112, D:G.113, D:Q.114, D:H.115, D:A.302 Salt bridges: D:K.87

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

EDO.8: 5 residues within 4Å: Chain A: F.107, N.108, G.110 Chain B: R.275, V.276 Ligand excluded by PLIP EDO.18: 6 residues within 4Å: Chain B: Q.36, K.37, D.38, P.39, Q.42 Ligands: EDO.24 Ligand excluded by PLIP EDO.19: 2 residues within 4Å: Chain B: R.363, E.364 Ligand excluded by PLIP EDO.21: 1 residues within 4Å: Chain B: D.218 Ligand excluded by PLIP EDO.24: 3 residues within 4Å: Chain B: Q.36, Q.42 Ligands: EDO.18 Ligand excluded by PLIP EDO.28: 4 residues within 4Å: Chain B: Q.44, L.48, L.126 Ligands: PEG.25 Ligand excluded by PLIP EDO.29: 5 residues within 4Å: Chain B: P.56, E.211, A.214, Q.215 Ligands: DMS.14 Ligand excluded by PLIP EDO.30: 2 residues within 4Å: Chain B: S.143, P.144 Ligand excluded by PLIP EDO.31: 5 residues within 4Å: Chain B: R.70, E.367, K.368, E.369 Chain D: I.319 Ligand excluded by PLIP EDO.46: 5 residues within 4Å: Chain C: F.107, N.108, G.110 Chain D: R.275, V.276 Ligand excluded by PLIP EDO.56: 6 residues within 4Å: Chain D: Q.36, K.37, D.38, P.39, Q.42 Ligands: EDO.62 Ligand excluded by PLIP EDO.57: 2 residues within 4Å: Chain D: R.363, E.364 Ligand excluded by PLIP EDO.59: 1 residues within 4Å: Chain D: D.218 Ligand excluded by PLIP EDO.62: 3 residues within 4Å: Chain D: Q.36, Q.42 Ligands: EDO.56 Ligand excluded by PLIP EDO.66: 4 residues within 4Å: Chain D: Q.44, L.48, L.126 Ligands: PEG.63 Ligand excluded by PLIP EDO.67: 5 residues within 4Å: Chain D: P.56, E.211, A.214, Q.215 Ligands: DMS.52 Ligand excluded by PLIP EDO.68: 2 residues within 4Å: Chain D: S.143, P.144 Ligand excluded by PLIP EDO.69: 5 residues within 4Å: Chain B: I.319 Chain D: R.70, E.367, K.368, E.369 Ligand excluded by PLIP

10 x CS: CESIUM ION(Non-covalent)

CS.10: 4 residues within 4Å: Chain A: A.167, G.170, H.204, A.206 No protein-ligand interaction detected (PLIP) CS.11: 3 residues within 4Å: Chain A: S.221, A.265, R.267 No protein-ligand interaction detected (PLIP) CS.33: 2 residues within 4Å: Chain B: D.225, S.249 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.249, H2O.30 CS.34: 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.35: 3 residues within 4Å: Chain B: T.66, T.69, T.71 No protein-ligand interaction detected (PLIP) CS.48: 4 residues within 4Å: Chain C: A.167, G.170, H.204, A.206 No protein-ligand interaction detected (PLIP) CS.49: 3 residues within 4Å: Chain C: S.221, A.265, R.267 No protein-ligand interaction detected (PLIP) CS.71: 2 residues within 4Å: Chain D: D.225, S.249 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:S.249, H2O.63 CS.72: 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 CS.73: 3 residues within 4Å: Chain D: T.66, T.69, T.71 No protein-ligand interaction detected (PLIP)

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

CL.12: 4 residues within 4Å: Chain A: E.2, R.3, Y.4, E.5 Ligand excluded by PLIP CL.36: 1 residues within 4Å: Chain B: D.323 Ligand excluded by PLIP CL.37: 2 residues within 4Å: Chain B: R.141, P.144 Ligand excluded by PLIP CL.38: 2 residues within 4Å: Chain B: Y.8, G.10 Ligand excluded by PLIP CL.50: 4 residues within 4Å: Chain C: E.2, R.3, Y.4, E.5 Ligand excluded by PLIP CL.74: 1 residues within 4Å: Chain D: D.323 Ligand excluded by PLIP CL.75: 2 residues within 4Å: Chain D: R.141, P.144 Ligand excluded by PLIP CL.76: 2 residues within 4Å: Chain D: Y.8, G.10 Ligand excluded by PLIP

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

PEG.17: 7 residues within 4Å: Chain B: H.273, G.274, R.275, M.286, M.287, Q.288, E.295 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.273, B:Q.288 Water bridges: B:Q.288 PEG.23: 4 residues within 4Å: Chain B: T.328, D.330, E.331, K.360 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.328, B:K.360 Water bridges: B:T.328, B:D.330, B:E.331, B:E.331 PEG.25: 6 residues within 4Å: Chain B: D.47, L.48, N.51, Y.52, L.125 Ligands: EDO.28 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.47 Water bridges: B:N.51 PEG.55: 7 residues within 4Å: Chain D: H.273, G.274, R.275, M.286, M.287, Q.288, E.295 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:H.273, D:Q.288 Water bridges: D:Q.288 PEG.61: 4 residues within 4Å: Chain D: T.328, D.330, E.331, K.360 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:K.360 Water bridges: D:T.328, D:D.330, D:E.331, D:E.331 PEG.63: 6 residues within 4Å: Chain D: D.47, L.48, N.51, Y.52, L.125 Ligands: EDO.66 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.47 Water bridges: D:N.51

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

PLP.32: 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: TRP.13 17 PLIP interactions: 16 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:A.85, B:K.87, B:A.348, W.13 Hydrogen bonds: B:G.232, B:G.233, B:G.234, B:S.235, B:N.236, B:N.236, B:S.377 Water bridges: B:S.235, B:S.235, B:A.237 Salt bridges: B:H.86, B:K.87 pi-Stacking: B:H.86 PLP.70: 19 residues within 4Å: Chain D: 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: TRP.51 18 PLIP interactions: 17 interactions with chain D, 1 Ligand-Ligand interactions Hydrophobic interactions: D:A.85, D:K.87, D:A.348, W.51 Hydrogen bonds: D:T.190, D:G.232, D:G.233, D:G.234, D:S.235, D:N.236, D:N.236, D:S.377 Water bridges: D:S.235, D:S.235, D:A.237 Salt bridges: D:H.86, D:K.87 pi-Stacking: D:H.86

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 inhibitor N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the enzyme alpha-site, cesium ion at the metal coordination site and the product L-tryptophan at the enzyme beta-site at 1.05 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

2022-02-02

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

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