SMTL ID : 7jhw.1

The internal aldimine crystal structure of Salmonella typhimurium Tryptophan Synthase mutant beta-S377A in complex with inhibitor 2-({[4-(trifluoromethoxy)phenyl]sulfonyl}amino)ethyl dihydrogen phosphate (F9F) at the alpha-site and Cesium ion at the metal coordination site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 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.37: 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

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

DMS.2: 6 residues within 4Å: Chain A: L.191, P.192, L.193, Q.210, A.222, A.226 Ligand excluded by PLIP DMS.3: 5 residues within 4Å: Chain A: N.12, E.16, V.224, A.228, A.268 Ligand excluded by PLIP DMS.4: 4 residues within 4Å: Chain A: S.55, L.69, F.72 Chain B: G.162 Ligand excluded by PLIP DMS.5: 9 residues within 4Å: Chain A: Y.115, V.128, V.131, S.136, F.139, R.140, P.150, I.151, F.152 Ligand excluded by PLIP DMS.6: 4 residues within 4Å: Chain A: P.217, F.258, A.261, M.262 Ligand excluded by PLIP DMS.7: 5 residues within 4Å: Chain A: I.41, H.92, P.93, T.94, I.95 Ligand excluded by PLIP DMS.8: 3 residues within 4Å: Chain A: A.43, R.256, S.260 Ligand excluded by PLIP DMS.9: 3 residues within 4Å: Chain A: Q.165, S.168, Y.169 Ligand excluded by PLIP DMS.14: 4 residues within 4Å: Chain B: Y.133, E.172, R.175, D.176 Ligand excluded by PLIP DMS.15: 2 residues within 4Å: Chain B: R.363, E.364 Ligand excluded by PLIP DMS.16: 5 residues within 4Å: Chain B: I.262, G.265, H.267, H.273 Ligands: DMS.20 Ligand excluded by PLIP DMS.17: 3 residues within 4Å: Chain B: Q.36, Q.42 Ligands: CL.32 Ligand excluded by PLIP DMS.18: 9 residues within 4Å: Chain B: P.56, T.57, A.58, Q.215 Chain D: K.50, G.54, R.55, P.56 Ligands: DMS.54 Ligand excluded by PLIP DMS.19: 2 residues within 4Å: Chain B: K.99, R.100 Ligand excluded by PLIP DMS.20: 8 residues within 4Å: Chain B: H.267, H.273, G.274, R.275, M.286, M.287, Q.288 Ligands: DMS.16 Ligand excluded by PLIP DMS.21: 5 residues within 4Å: Chain B: Q.42, F.45, A.46, L.49, M.207 Ligand excluded by PLIP DMS.23: 5 residues within 4Å: Chain B: F.385, H.388 Chain D: S.143, F.147 Ligands: DMS.62 Ligand excluded by PLIP DMS.24: 9 residues within 4Å: Chain B: R.141, E.296, S.297, Y.298, S.299, S.301, A.302, L.304, D.305 Ligand excluded by PLIP DMS.25: 2 residues within 4Å: Chain B: E.211, Q.215 Ligand excluded by PLIP DMS.26: 6 residues within 4Å: Chain B: S.143, V.146, F.147, R.150 Chain D: H.388 Ligands: DMS.59 Ligand excluded by PLIP DMS.38: 6 residues within 4Å: Chain C: L.191, P.192, L.193, Q.210, A.222, A.226 Ligand excluded by PLIP DMS.39: 5 residues within 4Å: Chain C: N.12, E.16, V.224, A.228, A.268 Ligand excluded by PLIP DMS.40: 4 residues within 4Å: Chain C: S.55, L.69, F.72 Chain D: G.162 Ligand excluded by PLIP DMS.41: 9 residues within 4Å: Chain C: Y.115, V.128, V.131, S.136, F.139, R.140, P.150, I.151, F.152 Ligand excluded by PLIP DMS.42: 4 residues within 4Å: Chain C: P.217, F.258, A.261, M.262 Ligand excluded by PLIP DMS.43: 5 residues within 4Å: Chain C: I.41, H.92, P.93, T.94, I.95 Ligand excluded by PLIP DMS.44: 3 residues within 4Å: Chain C: A.43, R.256, S.260 Ligand excluded by PLIP DMS.45: 3 residues within 4Å: Chain C: Q.165, S.168, Y.169 Ligand excluded by PLIP DMS.50: 4 residues within 4Å: Chain D: Y.133, E.172, R.175, D.176 Ligand excluded by PLIP DMS.51: 2 residues within 4Å: Chain D: R.363, E.364 Ligand excluded by PLIP DMS.52: 5 residues within 4Å: Chain D: I.262, G.265, H.267, H.273 Ligands: DMS.56 Ligand excluded by PLIP DMS.53: 3 residues within 4Å: Chain D: Q.36, Q.42 Ligands: CL.68 Ligand excluded by PLIP DMS.54: 9 residues within 4Å: Chain B: K.50, G.54, R.55, P.56 Chain D: P.56, T.57, A.58, Q.215 Ligands: DMS.18 Ligand excluded by PLIP DMS.55: 2 residues within 4Å: Chain D: K.99, R.100 Ligand excluded by PLIP DMS.56: 8 residues within 4Å: Chain D: H.267, H.273, G.274, R.275, M.286, M.287, Q.288 Ligands: DMS.52 Ligand excluded by PLIP DMS.57: 5 residues within 4Å: Chain D: Q.42, F.45, A.46, L.49, M.207 Ligand excluded by PLIP DMS.59: 5 residues within 4Å: Chain B: S.143, F.147 Chain D: F.385, H.388 Ligands: DMS.26 Ligand excluded by PLIP DMS.60: 9 residues within 4Å: Chain D: R.141, E.296, S.297, Y.298, S.299, S.301, A.302, L.304, D.305 Ligand excluded by PLIP DMS.61: 2 residues within 4Å: Chain D: E.211, Q.215 Ligand excluded by PLIP DMS.62: 6 residues within 4Å: Chain B: H.388 Chain D: S.143, V.146, F.147, R.150 Ligands: DMS.23 Ligand excluded by PLIP

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

CL.10: 1 residues within 4Å: Chain A: F.114 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain A: R.140, Y.169 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain A: A.167, G.170, H.204 Ligand excluded by PLIP CL.29: 1 residues within 4Å: Chain B: G.274 Ligand excluded by PLIP CL.30: 1 residues within 4Å: Chain B: R.150 Ligand excluded by PLIP CL.31: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.32: 3 residues within 4Å: Chain B: Q.36, K.37 Ligands: DMS.17 Ligand excluded by PLIP CL.33: 1 residues within 4Å: Chain B: E.11 Ligand excluded by PLIP CL.34: 3 residues within 4Å: Chain B: K.219, E.220, G.221 Ligand excluded by PLIP CL.35: 1 residues within 4Å: Chain B: F.9 Ligand excluded by PLIP CL.36: 2 residues within 4Å: Chain B: K.368, E.369 Ligand excluded by PLIP CL.46: 1 residues within 4Å: Chain C: F.114 Ligand excluded by PLIP CL.47: 2 residues within 4Å: Chain C: R.140, Y.169 Ligand excluded by PLIP CL.48: 3 residues within 4Å: Chain C: A.167, G.170, H.204 Ligand excluded by PLIP CL.65: 1 residues within 4Å: Chain D: G.274 Ligand excluded by PLIP CL.66: 1 residues within 4Å: Chain D: R.150 Ligand excluded by PLIP CL.67: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.68: 3 residues within 4Å: Chain D: Q.36, K.37 Ligands: DMS.53 Ligand excluded by PLIP CL.69: 1 residues within 4Å: Chain D: E.11 Ligand excluded by PLIP CL.70: 3 residues within 4Å: Chain D: K.219, E.220, G.221 Ligand excluded by PLIP CL.71: 1 residues within 4Å: Chain D: F.9 Ligand excluded by PLIP CL.72: 2 residues within 4Å: Chain D: K.368, E.369 Ligand excluded by PLIP

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

PLP.13: 15 residues within 4Å: Chain B: A.85, H.86, K.87, T.190, G.232, G.233, G.234, S.235, N.236, G.303, L.304, E.350, S.351, A.377, G.378 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:K.87, B:A.377 Hydrogen bonds: B:H.86, B:T.190, B:G.232, B:G.233, B:G.234, B:S.235, B:N.236, B:N.236 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.49: 15 residues within 4Å: Chain D: A.85, H.86, K.87, T.190, G.232, G.233, G.234, S.235, N.236, G.303, L.304, E.350, S.351, A.377, G.378 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:K.87, D:A.377 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 Water bridges: D:S.235, D:S.235, 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.22: 5 residues within 4Å: Chain B: I.65, T.338, H.342, M.362, R.363 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.363, B:R.363 EDO.58: 5 residues within 4Å: Chain D: I.65, T.338, H.342, M.362, R.363 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.363, D:R.363

4 x CS: CESIUM ION(Non-covalent)

CS.27: 6 residues within 4Å: Chain B: V.231, G.232, E.256, G.268, P.270, S.308 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:G.232, H2O.24 CS.28: 3 residues within 4Å: Chain B: T.66, T.69, T.71 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:T.71, H2O.28 CS.63: 6 residues within 4Å: Chain D: V.231, G.232, E.256, G.268, P.270, S.308 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:G.232, H2O.59 CS.64: 3 residues within 4Å: Chain D: T.66, T.69, T.71 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:T.71, H2O.63

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hilario, E. et al., The internal aldimine crystal structure of Salmonella typhimurium Tryptophan Synthase mutant beta-S377A in complex with inhibitor 2-({[4-(trifluoromethoxy)phenyl]sulfonyl}amino)ethyl dihydrogen phosphate (F9F) at the alpha-site and Cesium ion at the metal coordination site. To be Published

Release Date

2021-07-28

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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