SMTL ID : 5cgq.1

Crystal structure of Tryptophan Synthase from Salmonella typhimurium in complex with F9 ligand in the alpha-site and the product L-Tryptophan in the beta-site.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.18 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.9: 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

6 x CS: CESIUM ION(Non-covalent)

CS.2: 3 residues within 4Å: Chain A: S.221, A.265, R.267 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:A.265, A:R.267, H2O.1, H2O.9, H2O.11 CS.6: 7 residues within 4Å: Chain B: V.231, G.232, G.268, P.270, L.304, F.306, S.308 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:G.232, B:F.306, H2O.19 CS.7: 3 residues within 4Å: Chain B: T.66, T.69, T.71 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.66, B:T.69, B:T.71, H2O.21, H2O.25 CS.10: 3 residues within 4Å: Chain C: S.221, A.265, R.267 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:A.265, C:R.267, H2O.31, H2O.39, H2O.41 CS.14: 7 residues within 4Å: Chain D: V.231, G.232, G.268, P.270, L.304, F.306, S.308 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:G.232, D:F.306, H2O.49 CS.15: 3 residues within 4Å: Chain D: T.66, T.69, T.71 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:T.66, D:T.69, D:T.71, H2O.51, H2O.56

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: TRP.4 19 PLIP interactions: 18 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:A.85, B:K.87, B:A.348, W.4 Hydrogen bonds: B:K.87, 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:S.235, B:S.235, B:A.237 Salt bridges: B:H.86, B:K.87 pi-Stacking: B:H.86 PLP.11: 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.12 20 PLIP interactions: 1 Ligand-Ligand interactions, 19 interactions with chain D Hydrophobic interactions: W.12, D:A.85, D:K.87, D:A.348 Hydrogen bonds: 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:K.87, D:S.235, D:S.235, D:A.237 Salt bridges: D:H.86, D:K.87 pi-Stacking: D:H.86

2 x TRP: TRYPTOPHAN(Non-covalent)

TRP.4: 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.3 12 PLIP interactions: 12 interactions with chain B, Hydrophobic interactions: B:L.166, B:T.190, B:F.306, B:F.306 Hydrogen bonds: 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.12: 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.11 12 PLIP interactions: 12 interactions with chain D, Hydrophobic interactions: D:L.166, D:T.190, D:F.306, D:F.306 Hydrogen bonds: 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

2 x BCN: BICINE(Non-covalent)

BCN.5: 8 residues within 4Å: Chain B: T.248, S.249, V.250, G.251, L.252, G.320, R.321, D.323 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.249, B:L.252, B:L.252, B:R.321, B:R.321 Salt bridges: B:R.321, B:D.323 BCN.13: 8 residues within 4Å: Chain D: T.248, S.249, V.250, G.251, L.252, G.320, R.321, D.323 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:S.249, D:L.252, D:L.252, D:R.321, D:R.321 Salt bridges: D:R.321, D:D.323

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

EDO.8: 3 residues within 4Å: Chain B: T.3, L.5, N.6 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.3 Water bridges: B:T.3 EDO.16: 3 residues within 4Å: Chain D: T.3, L.5, N.6 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.3, D:T.3 Water bridges: D:T.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hilario, E. et al., Crystal structure of Tryptophan Synthase from Salmonella typhimurium in complex with F9 ligand and the product L-Tryptophan in the beta-site. To Be Published

Release Date

2016-07-13

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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