SMTL ID : 4zqc.1

Tryptophan Synthase from Salmonella typhimurium in complex with two molecules of N-(4'-trifluoromethoxybenzoyl)-2-amino-1-ethylphosphate (F6F) inhibitor in the alpha-site and a single F6F molecule in the beta-site at 1.54 Angstrom resolution.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.54 Å

Oligo State

hetero-2-2-mer

Ligands

6 x F6F: 2-{[4-(TRIFLUOROMETHOXY)BENZOYL]AMINO}ETHYL DIHYDROGEN PHOSPHATE(Non-covalent)

F6F.1: 17 residues within 4Å: Chain A: F.22, E.49, A.59, D.60, L.100, L.127, A.129, I.153, Y.175, F.212, G.213, I.232, S.233, G.234, S.235 Chain B: P.18 Ligands: F6F.2 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.100, A:L.100, A:L.127, A:I.153, A:Y.175 Hydrogen bonds: A:F.212, A:G.213, A:G.234, A:S.235 Water bridges: A:I.214, A:I.214, A:S.235, A:S.235, A:A.236 pi-Stacking: A:F.212 F6F.2: 14 residues within 4Å: Chain A: L.58, A.59, D.60, G.61, I.64, F.212, S.235 Chain B: P.18, I.20, L.21, L.174, R.175, S.178 Ligands: F6F.1 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:A.59, A:F.212, B:P.18, B:I.20 Hydrogen bonds: A:D.60, A:G.61, B:S.178 Water bridges: A:S.235, A:S.235 Halogen bonds: A:L.58 F6F.7: 17 residues within 4Å: Chain B: K.87, E.109, T.110, G.111, Q.114, H.115, C.170, L.174, Y.186, L.188, G.189, T.190, G.193, P.194, F.280, F.306 Ligands: PLP.6 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:E.109, B:L.188, B:T.190, B:F.306, B:F.306 Hydrogen bonds: B:E.109, B:E.109, B:G.111, B:A.112, B:G.113, B:Q.114, B:H.115 Water bridges: B:K.87 Salt bridges: B:K.87 Halogen bonds: B:Y.186 F6F.18: 17 residues within 4Å: Chain C: F.22, E.49, A.59, D.60, L.100, L.127, A.129, I.153, Y.175, F.212, G.213, I.232, S.233, G.234, S.235 Chain D: P.18 Ligands: F6F.19 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:L.100, C:L.100, C:L.127, C:I.153, C:Y.175 Hydrogen bonds: C:Y.175, C:F.212, C:G.213, C:G.234, C:S.235 Water bridges: C:I.214, C:I.214, C:S.235, C:S.235, C:A.236 pi-Stacking: C:F.212 F6F.19: 14 residues within 4Å: Chain C: L.58, A.59, D.60, G.61, I.64, F.212, S.235 Chain D: P.18, I.20, L.21, L.174, R.175, S.178 Ligands: F6F.18 11 PLIP interactions: 8 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:A.59, C:F.212, D:P.18, D:I.20 Hydrogen bonds: C:D.60, C:D.60, C:G.61, D:S.178 Water bridges: C:S.235, C:S.235 Halogen bonds: C:L.58 F6F.24: 17 residues within 4Å: Chain D: K.87, E.109, T.110, G.111, Q.114, H.115, C.170, L.174, Y.186, L.188, G.189, T.190, G.193, P.194, F.280, F.306 Ligands: PLP.23 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:E.109, D:L.188, D:T.190, D:F.306, D:F.306 Hydrogen bonds: D:E.109, D:T.110, D:G.111, D:A.112, D:G.113, D:Q.114, D:H.115 Water bridges: D:K.87, D:T.190 Salt bridges: D:K.87 Halogen bonds: D:Y.186

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

DMS.3: 8 residues within 4Å: Chain A: F.22, T.24, G.51, V.52, D.60, I.64, N.68, L.100 Ligand excluded by PLIP DMS.4: 5 residues within 4Å: Chain A: M.1, N.147, I.148, A.149, R.171 Ligand excluded by PLIP DMS.5: 5 residues within 4Å: Chain A: N.12, R.15, E.16, G.17, V.224 Ligand excluded by PLIP DMS.9: 4 residues within 4Å: Chain B: T.66, T.69, T.71, T.72 Ligand excluded by PLIP DMS.10: 7 residues within 4Å: Chain B: H.267, H.273, G.274, M.286, M.287, Q.288, E.295 Ligand excluded by PLIP DMS.11: 5 residues within 4Å: Chain B: T.60, K.61 Chain D: D.47, L.48, N.51 Ligand excluded by PLIP DMS.12: 5 residues within 4Å: Chain B: Q.42, F.45, A.46, L.49, M.207 Ligand excluded by PLIP DMS.13: 2 residues within 4Å: Chain B: T.328, E.331 Ligand excluded by PLIP DMS.14: 5 residues within 4Å: Chain B: A.112, Q.114, Q.142, K.382, D.383 Ligand excluded by PLIP DMS.15: 4 residues within 4Å: Chain B: R.150, L.151 Chain D: R.341, I.397 Ligand excluded by PLIP DMS.16: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP DMS.17: 5 residues within 4Å: Chain B: Q.36, K.37, D.38, P.39, Q.42 Ligand excluded by PLIP DMS.20: 8 residues within 4Å: Chain C: F.22, T.24, G.51, V.52, D.60, I.64, N.68, L.100 Ligand excluded by PLIP DMS.21: 5 residues within 4Å: Chain C: M.1, N.147, I.148, A.149, R.171 Ligand excluded by PLIP DMS.22: 5 residues within 4Å: Chain C: N.12, R.15, E.16, G.17, V.224 Ligand excluded by PLIP DMS.26: 4 residues within 4Å: Chain D: T.66, T.69, T.71, T.72 Ligand excluded by PLIP DMS.27: 7 residues within 4Å: Chain D: H.267, H.273, G.274, M.286, M.287, Q.288, E.295 Ligand excluded by PLIP DMS.28: 5 residues within 4Å: Chain B: D.47, L.48, N.51 Chain D: T.60, K.61 Ligand excluded by PLIP DMS.29: 5 residues within 4Å: Chain D: Q.42, F.45, A.46, L.49, M.207 Ligand excluded by PLIP DMS.30: 2 residues within 4Å: Chain D: T.328, E.331 Ligand excluded by PLIP DMS.31: 5 residues within 4Å: Chain D: A.112, Q.114, Q.142, K.382, D.383 Ligand excluded by PLIP DMS.32: 4 residues within 4Å: Chain B: R.341, I.397 Chain D: R.150, L.151 Ligand excluded by PLIP DMS.33: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP DMS.34: 5 residues within 4Å: Chain D: Q.36, K.37, D.38, P.39, Q.42 Ligand excluded by PLIP

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

PLP.6: 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, A.348, E.350, S.377, G.378 Ligands: F6F.7 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:A.85, B:K.87, B:A.348, B:E.350 Hydrogen bonds: B:Q.114, 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 pi-Stacking: B:H.86 PLP.23: 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, A.348, E.350, S.377, G.378 Ligands: F6F.24 19 PLIP interactions: 19 interactions with chain D Hydrophobic interactions: D:A.85, D:K.87, D:A.348, D:E.350 Hydrogen bonds: D:K.87, D:Q.114, 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:T.190, D:T.190, D:A.237 Salt bridges: D:H.86 pi-Stacking: D:H.86

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

NA.8: 4 residues within 4Å: Chain B: G.232, P.270, F.306, S.308 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.308 NA.25: 4 residues within 4Å: Chain D: G.232, P.270, F.306, S.308 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.232

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hilario, E. et al., Visualizing the tunnel in tryptophan synthase with crystallography: Insights into a selective filter for accommodating indole and rejecting water. Biochim.Biophys.Acta (2016)

Release Date

2016-02-10

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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