SMTL ID : 7ku9.1

The internal aldimine form of the wild-type Salmonella typhimurium Tryptophan Synthase with sodium ion at the metal coordination site, two molecules of F6F inhibitor at the enzyme alpha-site and another F6F molecule at the enzyme beta-site at 1.40 Angstrom resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

hetero-1-1-mer

Ligands

3 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, 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 Ligands: F6F.9 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.100, A:I.153, 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:S.235 pi-Stacking: A:F.212 F6F.9: 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 8 PLIP interactions: 1 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:S.178, A:A.59, A:D.60, A:G.61 Hydrophobic interactions: A:A.59, A:F.212 Water bridges: A:I.64 Halogen bonds: A:L.58 F6F.14: 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.13 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:T.110, B:G.111, B:A.112, B:G.113, B:Q.114, B:H.115 Water bridges: B:T.190 Salt bridges: B:K.87 Halogen bonds: B:Y.186

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

DMS.2: 6 residues within 4Å: Chain A: M.1, D.124, N.147, I.148, A.149, R.171 Ligand excluded by PLIP DMS.4: 10 residues within 4Å: Chain A: F.22, T.24, G.51, V.52, F.54, D.60, I.64, N.68, L.100, Y.102 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.6: 6 residues within 4Å: Chain A: I.30, L.34, Q.80, E.83, M.84, L.87 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.12: 6 residues within 4Å: Chain A: F.107, I.111, P.138, F.139 Chain B: Y.16, K.283 Ligand excluded by PLIP DMS.15: 4 residues within 4Å: Chain B: T.3, L.4, L.5, N.6 Ligand excluded by PLIP DMS.16: 5 residues within 4Å: Chain B: Q.42, F.45, A.46, L.49, M.207 Ligand excluded by PLIP DMS.17: 3 residues within 4Å: Chain B: Q.36, Q.42 Ligands: DMS.30 Ligand excluded by PLIP DMS.18: 5 residues within 4Å: Chain B: I.65, T.338, H.342, M.362, R.363 Ligand excluded by PLIP DMS.19: 3 residues within 4Å: Chain B: E.172, R.175, D.176 Ligand excluded by PLIP DMS.20: 4 residues within 4Å: Chain B: I.262, H.267, H.273 Ligands: DMS.31 Ligand excluded by PLIP DMS.21: 3 residues within 4Å: Chain B: Y.8, G.10, E.11 Ligand excluded by PLIP DMS.22: 1 residues within 4Å: Chain B: H.260 Ligand excluded by PLIP DMS.23: 3 residues within 4Å: Chain B: I.384, F.385, H.388 Ligand excluded by PLIP DMS.25: 5 residues within 4Å: Chain B: T.248, S.249, V.250, G.251, R.321 Ligand excluded by PLIP DMS.27: 3 residues within 4Å: Chain B: G.127, L.128, K.129 Ligand excluded by PLIP DMS.28: 5 residues within 4Å: Chain B: A.112, Q.114, Q.142, K.382, D.383 Ligand excluded by PLIP DMS.29: 3 residues within 4Å: Chain B: H.357, M.361, E.364 Ligand excluded by PLIP DMS.30: 6 residues within 4Å: Chain B: Q.36, K.37, D.38, P.39, Q.42 Ligands: DMS.17 Ligand excluded by PLIP DMS.31: 8 residues within 4Å: Chain B: H.267, H.273, G.274, M.286, M.287, Q.288, E.295 Ligands: DMS.20 Ligand excluded by PLIP DMS.32: 7 residues within 4Å: Chain B: P.270, L.271, K.272, G.274, R.275, V.276, P.285 Ligand excluded by PLIP DMS.33: 5 residues within 4Å: Chain B: T.66, G.68, T.69, T.71, T.72 Ligand excluded by PLIP DMS.35: 4 residues within 4Å: Chain B: P.56, E.211, A.214, Q.215 Ligand excluded by PLIP

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

EDO.3: 4 residues within 4Å: Chain A: P.78, A.79, F.82, F.114 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:P.78 Water bridges: A:A.79, A:L.105, A:V.106, A:N.109, A:N.109 EDO.8: 1 residues within 4Å: Chain A: R.225 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.225, A:R.225 EDO.10: 3 residues within 4Å: Chain A: A.43, R.256, S.260 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.43, A:R.256 EDO.36: 3 residues within 4Å: Chain B: F.147, R.150, L.151 1 PLIP interactions: 1 interactions with chain B Water bridges: B:L.151 EDO.37: 4 residues within 4Å: Chain B: G.83, G.84, R.379, K.382 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.83 Water bridges: B:R.148, B:R.379, B:R.379 EDO.38: 2 residues within 4Å: Chain B: A.290, D.291 No protein-ligand interaction detected (PLIP) EDO.41: 2 residues within 4Å: Chain B: F.9, Y.315 3 PLIP interactions: 3 interactions with chain B Water bridges: B:G.10, B:Q.312, B:Q.312

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

CL.11: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.43: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.44: 1 residues within 4Å: Chain B: G.395 Ligand excluded by PLIP

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

PLP.13: 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.14 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:A.85, B:K.87, B:A.348, B:E.350 Hydrogen bonds: B:K.87, B:Q.114, 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 pi-Stacking: B:H.86

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

PEG.24: 5 residues within 4Å: Chain B: K.213, D.243, N.246, D.247, T.248 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:K.213, B:K.213, B:N.246, B:T.248 Water bridges: B:N.246, B:D.247, B:S.249 PEG.26: 5 residues within 4Å: Chain B: L.59, T.60, K.61, Y.74, K.219 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.61 Water bridges: B:K.61 PEG.34: 4 residues within 4Å: Chain B: D.218, K.219, E.220, G.221 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.218, B:E.220

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.39: 2 residues within 4Å: Chain B: R.363, E.364 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.363 GOL.40: 7 residues within 4Å: Chain B: L.5, N.6, Y.8, F.9, H.195, T.199, R.202 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.8, B:R.202, B:R.202 Water bridges: B:Q.312

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

NA.42: 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:S.308, B:S.308

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hilario, E. et al., The internal aldimine form of the wild-type Salmonella typhimurium Tryptophan Synthase with sodium ion at the metal coordination site, two molecules of F6F inhibitor at the enzyme alpha-site and another F6F molecule at the enzyme beta-site at 1.40 Angstrom resolution. To be Published

Release Date

2021-12-15

Peptides

Tryptophan synthase alpha chain: A
Tryptophan synthase beta chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Tryptophan synthase alpha chain

Tryptophan synthase beta chain

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