SMTL ID : 4wx2.1

Crystal structure of Tryptophan Synthase from Salmonella typhimurium in complex with two F6F molecules in the alpha-site and one F6F molecule in the beta-site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 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 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: 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 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 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:I.20, A:A.59, A:F.212 Hydrogen bonds: B:S.178, A:D.60, A:G.61 Water bridges: A:I.64 F6F.6: 19 residues within 4Å: Chain B: K.87, E.109, T.110, G.111, A.112, G.113, 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.3 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:E.109, B:L.188, B:T.190, 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:G.116 Water bridges: B:K.87, B:T.190 Salt bridges: B:K.87 Halogen bonds: B:Y.186 F6F.8: 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.9 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:L.100, C:Y.175 Hydrogen bonds: C:F.212, C:G.213, C:G.234, C:S.235 Water bridges: C:I.214, C:I.214 pi-Stacking: C:F.212 F6F.9: 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.8 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:A.59, C:F.212, D:I.20 Hydrogen bonds: C:G.61, D:S.178 Water bridges: C:I.64 F6F.13: 19 residues within 4Å: Chain D: K.87, E.109, T.110, G.111, A.112, G.113, 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.10 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:E.109, D:L.188, D:T.190, 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:G.116 Water bridges: D:K.87 Salt bridges: D:K.87 Halogen bonds: D:Y.186

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

PLP.3: 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: F6F.6 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:A.85, B:K.87, B:A.348, B:E.350 Hydrogen bonds: B:T.190, B:G.232, B:G.233, B:G.234, B:S.235, B:N.236, B:N.236, B:S.377 Water bridges: B:T.190, B:T.190, B:A.237 Salt bridges: B:H.86, B:K.87 pi-Stacking: B:H.86 PLP.10: 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: F6F.13 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:A.85, D:K.87, D:A.348, D:E.350 Hydrogen bonds: D:T.190, 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:A.237 Salt bridges: D:H.86, D:K.87 pi-Stacking: D:H.86

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

EDO.4: 2 residues within 4Å: Chain B: T.3, N.6 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.3 Water bridges: B:T.3 EDO.11: 2 residues within 4Å: Chain D: T.3, N.6 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.3 Water bridges: D:T.3

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

PEG.5: 3 residues within 4Å: Chain B: E.211, A.214, Q.215 1 PLIP interactions: 1 interactions with chain B Water bridges: B:D.218 PEG.12: 3 residues within 4Å: Chain D: E.211, A.214, Q.215 1 PLIP interactions: 1 interactions with chain D Water bridges: D:D.218

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

NA.7: 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:G.232 NA.14: 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:F.306

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

2015-11-18

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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