SMTL ID : 4ht3.1

The crystal structure of Salmonella typhimurium Tryptophan Synthase at 1.30A complexed with N-(4'-TRIFLUOROMETHOXYBENZENESULFONYL)-2-AMINO-1-ETHYLPHOSPHATE (F9) inhibitor in the alpha site, internal aldimine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

hetero-2-2-mer

Ligands

2 x F9F: 2-({[4-(TRIFLUOROMETHOXY)PHENYL]SULFONYL}AMINO)ETHYL DIHYDROGEN PHOSPHATE(Non-covalent)

F9F.1: 19 residues within 4Å: Chain A: F.22, E.49, A.59, I.64, L.100, L.127, A.129, I.153, Y.175, L.177, 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.33: 19 residues within 4Å: Chain C: F.22, E.49, A.59, I.64, L.100, L.127, A.129, I.153, Y.175, L.177, 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

8 x BCN: BICINE(Non-covalent)

BCN.2: 4 residues within 4Å: Chain A: S.247, P.248, K.249, Q.250 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.249, A:Q.250, A:Q.250 Salt bridges: A:K.249 BCN.14: 8 residues within 4Å: Chain B: G.259, H.260, E.263, T.328, D.329, D.330 Ligands: EDO.22, EDO.23 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.263, B:T.328, B:D.330 Water bridges: B:D.329 Salt bridges: B:D.330 BCN.15: 9 residues within 4Å: Chain B: T.248, S.249, V.250, G.251, L.252, G.320, R.321, D.323 Ligands: CL.31 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.249, B:L.252, B:L.252, B:R.321 Salt bridges: B:R.321, B:D.323 BCN.16: 5 residues within 4Å: Chain A: T.77 Chain B: T.289, A.290, D.291, Q.293 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:A.290, B:D.291, B:D.291, B:D.291 Water bridges: B:D.291 Salt bridges: B:D.291 BCN.34: 4 residues within 4Å: Chain C: S.247, P.248, K.249, Q.250 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.249, C:Q.250, C:Q.250 Salt bridges: C:K.249 BCN.46: 8 residues within 4Å: Chain D: G.259, H.260, E.263, T.328, D.329, D.330 Ligands: EDO.54, EDO.55 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:E.263, D:D.330, D:D.330 Salt bridges: D:D.330 BCN.47: 9 residues within 4Å: Chain D: T.248, S.249, V.250, G.251, L.252, G.320, R.321, D.323 Ligands: CL.63 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:S.249, D:L.252, D:L.252, D:R.321 Salt bridges: D:R.321, D:D.323 BCN.48: 5 residues within 4Å: Chain C: T.77 Chain D: T.289, A.290, D.291, Q.293 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:T.289, D:A.290, D:D.291, D:D.291 Water bridges: D:D.291 Salt bridges: D:D.291

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

CL.3: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.13: 1 residues within 4Å: Chain B: A.67 Ligand excluded by PLIP CL.17: 3 residues within 4Å: Chain B: G.83, V.117 Chain D: I.346 Ligand excluded by PLIP CL.27: 2 residues within 4Å: Chain B: Y.8, G.10 Ligand excluded by PLIP CL.29: 3 residues within 4Å: Chain B: D.225, K.368 Ligands: CL.31 Ligand excluded by PLIP CL.31: 4 residues within 4Å: Chain B: D.225, S.249 Ligands: BCN.15, CL.29 Ligand excluded by PLIP CL.32: 4 residues within 4Å: Chain B: F.12, V.276, P.285 Ligands: PGE.12 Ligand excluded by PLIP CL.35: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.45: 1 residues within 4Å: Chain D: A.67 Ligand excluded by PLIP CL.49: 3 residues within 4Å: Chain B: I.346 Chain D: G.83, V.117 Ligand excluded by PLIP CL.59: 2 residues within 4Å: Chain D: Y.8, G.10 Ligand excluded by PLIP CL.61: 3 residues within 4Å: Chain D: D.225, K.368 Ligands: CL.63 Ligand excluded by PLIP CL.63: 4 residues within 4Å: Chain D: D.225, S.249 Ligands: BCN.47, CL.61 Ligand excluded by PLIP CL.64: 4 residues within 4Å: Chain D: F.12, V.276, P.285 Ligands: PGE.44 Ligand excluded by PLIP

6 x CS: CESIUM ION(Non-covalent)

CS.4: 3 residues within 4Å: Chain A: S.221, A.265, R.267 No protein-ligand interaction detected (PLIP) CS.20: 3 residues within 4Å: Chain B: T.66, T.69, T.71 No protein-ligand interaction detected (PLIP) CS.21: 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 CS.36: 3 residues within 4Å: Chain C: S.221, A.265, R.267 No protein-ligand interaction detected (PLIP) CS.52: 3 residues within 4Å: Chain D: T.66, T.69, T.71 No protein-ligand interaction detected (PLIP) CS.53: 6 residues within 4Å: Chain D: V.231, G.232, E.256, G.268, P.270, S.308 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:G.232

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

PGE.5: 7 residues within 4Å: Chain A: F.107, I.111, E.135, P.138, F.139 Chain B: Y.16, K.283 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:Y.16, B:K.283, A:E.135 Water bridges: B:Y.8, A:D.112, A:R.145 PGE.12: 7 residues within 4Å: Chain B: P.270, L.271, K.272, G.274, P.285, N.317 Ligands: CL.32 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.317 PGE.26: 5 residues within 4Å: Chain B: E.210, E.211, A.214, Q.215, D.218 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.210 Water bridges: B:D.218 PGE.37: 7 residues within 4Å: Chain C: F.107, I.111, E.135, P.138, F.139 Chain D: Y.16, K.283 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:E.135, C:E.135, D:K.283 Water bridges: C:D.112, C:R.145, D:Y.16 PGE.44: 7 residues within 4Å: Chain D: P.270, L.271, K.272, G.274, P.285, N.317 Ligands: CL.64 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.317 PGE.58: 5 residues within 4Å: Chain D: E.210, E.211, A.214, Q.215, D.218 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.210 Water bridges: D:D.218

2 x PG5: 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE(Non-covalent)

PG5.6: 11 residues within 4Å: Chain A: R.164, V.166, A.167, S.168, G.170, R.171, T.174, Y.203, H.204, A.205, A.206 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.206 Water bridges: A:R.171 PG5.38: 11 residues within 4Å: Chain C: R.164, V.166, A.167, S.168, G.170, R.171, T.174, Y.203, H.204, A.205, A.206 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:A.206 Water bridges: C:R.171

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

EDO.7: 2 residues within 4Å: Chain A: P.93 Ligands: EDO.8 Ligand excluded by PLIP EDO.8: 3 residues within 4Å: Chain A: P.93, T.94 Ligands: EDO.7 Ligand excluded by PLIP EDO.9: 3 residues within 4Å: Chain A: A.86, L.87, E.90 Ligand excluded by PLIP EDO.11: 8 residues within 4Å: Chain B: K.87, T.110, G.111, A.112, G.113, Q.114, H.115 Ligands: EDO.28 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain B: K.61, K.219 Chain D: D.47, N.51 Ligands: PEG.25 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain B: I.262, H.273, V.325, S.326 Ligand excluded by PLIP EDO.22: 5 residues within 4Å: Chain B: D.330, E.331, E.334 Ligands: BCN.14, EDO.23 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain B: T.328, E.331 Ligands: BCN.14, EDO.22 Ligand excluded by PLIP EDO.28: 7 residues within 4Å: Chain B: E.109, H.115, L.166, C.170, G.189, T.190 Ligands: EDO.11 Ligand excluded by PLIP EDO.30: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EDO.39: 2 residues within 4Å: Chain C: P.93 Ligands: EDO.40 Ligand excluded by PLIP EDO.40: 3 residues within 4Å: Chain C: P.93, T.94 Ligands: EDO.39 Ligand excluded by PLIP EDO.41: 3 residues within 4Å: Chain C: A.86, L.87, E.90 Ligand excluded by PLIP EDO.43: 8 residues within 4Å: Chain D: K.87, T.110, G.111, A.112, G.113, Q.114, H.115 Ligands: EDO.60 Ligand excluded by PLIP EDO.50: 5 residues within 4Å: Chain B: D.47, N.51 Chain D: K.61, K.219 Ligands: PEG.57 Ligand excluded by PLIP EDO.51: 4 residues within 4Å: Chain D: I.262, H.273, V.325, S.326 Ligand excluded by PLIP EDO.54: 5 residues within 4Å: Chain D: D.330, E.331, E.334 Ligands: BCN.46, EDO.55 Ligand excluded by PLIP EDO.55: 4 residues within 4Å: Chain D: T.328, E.331 Ligands: BCN.46, EDO.54 Ligand excluded by PLIP EDO.60: 7 residues within 4Å: Chain D: E.109, H.115, L.166, C.170, G.189, T.190 Ligands: EDO.43 Ligand excluded by PLIP EDO.62: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

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

PLP.10: 18 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 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:A.85, B:K.87, B:A.348 Hydrogen bonds: 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: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 PLP.42: 18 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 19 PLIP interactions: 19 interactions with chain D Hydrophobic interactions: D:A.85, D:K.87, D:A.348 Hydrogen bonds: D:K.87, 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:S.235, D:S.235, D:A.237 Salt bridges: D:H.86, D:K.87 pi-Stacking: D:H.86

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

PEG.24: 4 residues within 4Å: Chain B: T.3, L.4, L.5, N.6 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.4 Water bridges: B:T.3 PEG.25: 8 residues within 4Å: Chain B: T.60, K.61, C.62, E.343 Chain D: N.51, Y.52, L.125 Ligands: EDO.18 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.61, B:E.343, B:E.343 Water bridges: B:Q.63 PEG.56: 4 residues within 4Å: Chain D: T.3, L.4, L.5, N.6 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.3, D:L.4 Water bridges: D:T.3 PEG.57: 8 residues within 4Å: Chain B: N.51, Y.52, L.125 Chain D: T.60, K.61, C.62, E.343 Ligands: EDO.50 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.61, D:E.343 Water bridges: D:Q.63

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Niks, D. et al., Allostery and substrate channeling in the tryptophan synthase bienzyme complex: evidence for two subunit conformations and four quaternary states. Biochemistry (2013)

Release Date

2014-01-01

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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