SMTL ID : 4y6g.1

Crystal structure of Tryptophan Synthase from Salmonella typhimurium in complex with N-(4'-trifluoromethoxybenzoyl)-2-amino-1-ethylphosphate (F6F) inhibitor in the alpha-site and beta-site.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

hetero-2-2-mer

Ligands

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

F6F.1: 16 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, F.212, G.213, S.233, G.234, S.235 Chain B: P.18 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:A.59, A:L.100, A:L.100, A:Y.175 Hydrogen bonds: A:Y.175, 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 F6F.3: 20 residues within 4Å: Chain B: K.87, E.109, T.110, G.111, A.112, G.113, Q.114, H.115, G.116, C.170, L.174, Y.186, L.188, G.189, T.190, G.193, P.194, F.280, F.306 Ligands: PLP.2 16 PLIP interactions: 16 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, B:G.116 Water bridges: B:G.303 Salt bridges: B:K.87 Halogen bonds: B:Y.186 F6F.5: 16 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, F.212, G.213, S.233, G.234, S.235 Chain D: P.18 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:A.59, C:L.100, C:L.100, 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:A.236 pi-Stacking: C:F.212 F6F.7: 20 residues within 4Å: Chain D: K.87, E.109, T.110, G.111, A.112, G.113, Q.114, H.115, G.116, C.170, L.174, Y.186, L.188, G.189, T.190, G.193, P.194, F.280, F.306 Ligands: PLP.6 17 PLIP interactions: 17 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, D:G.116 Water bridges: D:T.190, D:G.303 Salt bridges: D:K.87 Halogen bonds: D:Y.186

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

PLP.2: 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.3 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:A.85, B:K.87, B:A.348 Hydrogen bonds: 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 pi-Stacking: B:H.86 PLP.6: 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.7 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:A.85, D:K.87, D:A.348 Hydrogen bonds: 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, D:K.87 pi-Stacking: D:H.86

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

NA.4: 4 residues within 4Å: Chain B: G.232, P.270, F.306, S.308 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.306, B:S.308 NA.8: 4 residues within 4Å: Chain D: G.232, P.270, F.306, S.308 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.232, D:S.308

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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