SMTL ID : 7l47.1

The internal aldimine form of the beta-K167T mutant Tryptophan Synthase from Salmonella at 1.55 Angstrom resolution with cesium ion at the metal coordination site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

hetero-2-2-mer

Ligands

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

DMS.1: 9 residues within 4Å: Chain A: M.1, R.3, E.119, G.122, V.123, D.124, H.146, N.147, I.148 Ligand excluded by PLIP DMS.2: 8 residues within 4Å: Chain A: F.22, T.24, G.51, V.52, D.60, I.64, N.68, L.100 Ligand excluded by PLIP DMS.3: 3 residues within 4Å: Chain A: F.82, F.114, R.117 Ligand excluded by PLIP DMS.10: 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.47 Ligand excluded by PLIP DMS.11: 5 residues within 4Å: Chain B: Q.42, F.45, A.46, L.49, M.207 Ligand excluded by PLIP DMS.12: 3 residues within 4Å: Chain B: L.271, G.274, N.317 Ligand excluded by PLIP DMS.13: 2 residues within 4Å: Chain B: K.99, R.100 Ligand excluded by PLIP DMS.14: 3 residues within 4Å: Chain B: Q.36, Q.42 Ligands: DMS.15 Ligand excluded by PLIP DMS.15: 6 residues within 4Å: Chain B: Q.36, K.37, D.38, P.39, Q.42 Ligands: DMS.14 Ligand excluded by PLIP DMS.16: 10 residues within 4Å: Chain B: T.190, A.192, G.232, G.233, F.280, M.282, F.306, S.308, V.309, G.310 Ligand excluded by PLIP DMS.17: 5 residues within 4Å: Chain B: I.262, G.265, H.267, H.273 Ligands: EDO.22 Ligand excluded by PLIP DMS.18: 5 residues within 4Å: Chain B: S.143, V.146, F.147, R.150 Chain D: K.392 Ligand excluded by PLIP DMS.19: 5 residues within 4Å: Chain B: E.109, L.166, C.170, Y.279, F.280 Ligand excluded by PLIP DMS.20: 7 residues within 4Å: Chain B: T.110, G.111, A.112, G.113, Q.114, H.115 Ligands: PEG.8 Ligand excluded by PLIP DMS.38: 9 residues within 4Å: Chain C: M.1, R.3, E.119, G.122, V.123, D.124, H.146, N.147, I.148 Ligand excluded by PLIP DMS.39: 8 residues within 4Å: Chain C: F.22, T.24, G.51, V.52, D.60, I.64, N.68, L.100 Ligand excluded by PLIP DMS.40: 3 residues within 4Å: Chain C: F.82, F.114, R.117 Ligand excluded by PLIP DMS.47: 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.10 Ligand excluded by PLIP DMS.48: 5 residues within 4Å: Chain D: Q.42, F.45, A.46, L.49, M.207 Ligand excluded by PLIP DMS.49: 3 residues within 4Å: Chain D: L.271, G.274, N.317 Ligand excluded by PLIP DMS.50: 2 residues within 4Å: Chain D: K.99, R.100 Ligand excluded by PLIP DMS.51: 3 residues within 4Å: Chain D: Q.36, Q.42 Ligands: DMS.52 Ligand excluded by PLIP DMS.52: 6 residues within 4Å: Chain D: Q.36, K.37, D.38, P.39, Q.42 Ligands: DMS.51 Ligand excluded by PLIP DMS.53: 10 residues within 4Å: Chain D: T.190, A.192, G.232, G.233, F.280, M.282, F.306, S.308, V.309, G.310 Ligand excluded by PLIP DMS.54: 5 residues within 4Å: Chain D: I.262, G.265, H.267, H.273 Ligands: EDO.59 Ligand excluded by PLIP DMS.55: 5 residues within 4Å: Chain B: K.392 Chain D: S.143, V.146, F.147, R.150 Ligand excluded by PLIP DMS.56: 5 residues within 4Å: Chain D: E.109, L.166, C.170, Y.279, F.280 Ligand excluded by PLIP DMS.57: 7 residues within 4Å: Chain D: T.110, G.111, A.112, G.113, Q.114, H.115 Ligands: PEG.45 Ligand excluded by PLIP

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

EDO.4: 3 residues within 4Å: Chain A: L.100, I.153, Y.175 No protein-ligand interaction detected (PLIP) EDO.5: 4 residues within 4Å: Chain A: I.41, G.44, A.45, I.95 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.41 Water bridges: A:R.14 EDO.21: 5 residues within 4Å: Chain B: I.65, T.338, H.342, M.362, R.363 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.64, B:R.363 Water bridges: B:R.363 EDO.22: 4 residues within 4Å: Chain B: K.272, H.273, G.274 Ligands: DMS.17 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.274 EDO.23: 3 residues within 4Å: Chain B: K.219, E.220, G.221 No protein-ligand interaction detected (PLIP) EDO.24: 6 residues within 4Å: Chain B: H.273, G.274, R.275, M.286, M.287, Q.288 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.274, B:Q.288, B:Q.288 EDO.41: 3 residues within 4Å: Chain C: L.100, I.153, Y.175 No protein-ligand interaction detected (PLIP) EDO.42: 4 residues within 4Å: Chain C: I.41, G.44, A.45, I.95 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:I.41 Water bridges: C:R.14 EDO.58: 5 residues within 4Å: Chain D: I.65, T.338, H.342, M.362, R.363 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.64, D:R.363 Water bridges: D:R.363 EDO.59: 4 residues within 4Å: Chain D: K.272, H.273, G.274 Ligands: DMS.54 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:H.273, D:G.274 EDO.60: 3 residues within 4Å: Chain D: K.219, E.220, G.221 1 PLIP interactions: 1 interactions with chain D Water bridges: D:E.220 EDO.61: 6 residues within 4Å: Chain D: H.273, G.274, R.275, M.286, M.287, Q.288 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.274, D:Q.288, D:Q.288

6 x CS: CESIUM ION(Non-covalent)

CS.6: 3 residues within 4Å: Chain A: A.167, G.170, H.204 No protein-ligand interaction detected (PLIP) CS.25: 3 residues within 4Å: Chain B: T.66, T.69, T.71 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.71 CS.26: 7 residues within 4Å: Chain B: V.231, G.232, G.268, P.270, L.304, F.306, S.308 No protein-ligand interaction detected (PLIP) CS.43: 3 residues within 4Å: Chain C: A.167, G.170, H.204 No protein-ligand interaction detected (PLIP) CS.62: 3 residues within 4Å: Chain D: T.66, T.69, T.71 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.71 CS.63: 7 residues within 4Å: Chain D: V.231, G.232, G.268, P.270, L.304, F.306, S.308 No protein-ligand interaction detected (PLIP)

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

PLP.7: 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: PEG.8 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:A.85, B:K.87, B:A.348 Hydrogen bonds: B:Q.114, B:G.232, B:G.233, B:G.234, B:S.235, B:N.236, B:N.236, B:S.377 Water bridges: B:Q.114, B:T.190, B:T.190, B:S.235, B:S.235, B:A.237 Salt bridges: B:H.86 pi-Stacking: B:H.86 PLP.44: 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: PEG.45 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:A.85, D:K.87, D:A.348 Hydrogen bonds: D:Q.114, 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:Q.114, D:S.235, D:S.235, D:A.237 Salt bridges: D:H.86 pi-Stacking: D:H.86

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

PEG.8: 7 residues within 4Å: Chain B: K.87, G.189, T.190, G.303, F.306 Ligands: PLP.7, DMS.20 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.303 Water bridges: B:T.190, B:T.190 PEG.9: 1 residues within 4Å: Chain B: E.182 No protein-ligand interaction detected (PLIP) PEG.45: 7 residues within 4Å: Chain D: K.87, G.189, T.190, G.303, F.306 Ligands: PLP.44, DMS.57 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.303 Water bridges: D:T.190 PEG.46: 1 residues within 4Å: Chain D: E.182 No protein-ligand interaction detected (PLIP)

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

CL.27: 2 residues within 4Å: Chain B: G.83, R.379 Ligand excluded by PLIP CL.28: 1 residues within 4Å: Chain B: R.150 Ligand excluded by PLIP CL.29: 2 residues within 4Å: Chain B: R.175, D.176 Ligand excluded by PLIP CL.30: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.31: 2 residues within 4Å: Chain B: A.290, D.291 Ligand excluded by PLIP CL.32: 2 residues within 4Å: Chain B: F.9, Y.315 Ligand excluded by PLIP CL.33: 2 residues within 4Å: Chain D: F.385, H.388 Ligand excluded by PLIP CL.34: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.35: 4 residues within 4Å: Chain B: T.3, L.4, L.5, N.6 Ligand excluded by PLIP CL.36: 2 residues within 4Å: Chain B: G.127, L.128 Ligand excluded by PLIP CL.37: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.64: 2 residues within 4Å: Chain D: G.83, R.379 Ligand excluded by PLIP CL.65: 1 residues within 4Å: Chain D: R.150 Ligand excluded by PLIP CL.66: 2 residues within 4Å: Chain D: R.175, D.176 Ligand excluded by PLIP CL.67: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.68: 2 residues within 4Å: Chain D: A.290, D.291 Ligand excluded by PLIP CL.69: 2 residues within 4Å: Chain D: F.9, Y.315 Ligand excluded by PLIP CL.70: 2 residues within 4Å: Chain B: F.385, H.388 Ligand excluded by PLIP CL.71: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.72: 4 residues within 4Å: Chain D: T.3, L.4, L.5, N.6 Ligand excluded by PLIP CL.73: 2 residues within 4Å: Chain D: G.127, L.128 Ligand excluded by PLIP CL.74: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hilario, E. et al., The internal aldimine form of the beta-K167T mutant Tryptophan Synthase from Salmonella at 1.55 Angstrom resolution with cesium ion at the metal coordination site. To be Published

Release Date

2021-12-29

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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