SMTL ID : 7lt4.1

The aminoacrylate form of the beta-K167T mutant Tryptophan Synthase at 1.80 Angstrom resolution in complex with N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the enzyme alpha-site and cesium ion at the metal coordination site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-2-2-mer

Ligands

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

DMS.1: 8 residues within 4Å: Chain A: M.1, R.3, E.119, V.123, D.124, H.146, N.147, I.148 Ligand excluded by PLIP DMS.2: 8 residues within 4Å: Chain A: V.128, V.131, S.136, F.139, R.140, P.150, I.151, F.152 Ligand excluded by PLIP DMS.6: 8 residues within 4Å: Chain A: S.55, D.56 Chain B: S.163, T.167, D.168, Y.279, I.294, E.295 Ligand excluded by PLIP DMS.10: 10 residues within 4Å: Chain B: P.56, T.57, Q.215 Chain D: K.50, G.54, R.55, P.56 Ligands: CS.29, DMS.39, CS.58 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: N.64, T.338, H.342 Ligand excluded by PLIP DMS.13: 1 residues within 4Å: Chain B: E.331 Ligand excluded by PLIP DMS.14: 3 residues within 4Å: Chain B: I.262, H.267, H.273 Ligand excluded by PLIP DMS.15: 4 residues within 4Å: Chain B: Q.36, K.37, P.39, Q.42 Ligand excluded by PLIP DMS.30: 8 residues within 4Å: Chain C: M.1, R.3, E.119, V.123, D.124, H.146, N.147, I.148 Ligand excluded by PLIP DMS.31: 8 residues within 4Å: Chain C: V.128, V.131, S.136, F.139, R.140, P.150, I.151, F.152 Ligand excluded by PLIP DMS.35: 8 residues within 4Å: Chain C: S.55, D.56 Chain D: S.163, T.167, D.168, Y.279, I.294, E.295 Ligand excluded by PLIP DMS.39: 10 residues within 4Å: Chain B: K.50, G.54, R.55, P.56 Chain D: P.56, T.57, Q.215 Ligands: DMS.10, CS.29, CS.58 Ligand excluded by PLIP DMS.40: 5 residues within 4Å: Chain D: Q.42, F.45, A.46, L.49, M.207 Ligand excluded by PLIP DMS.41: 3 residues within 4Å: Chain D: N.64, T.338, H.342 Ligand excluded by PLIP DMS.42: 1 residues within 4Å: Chain D: E.331 Ligand excluded by PLIP DMS.43: 3 residues within 4Å: Chain D: I.262, H.267, H.273 Ligand excluded by PLIP DMS.44: 4 residues within 4Å: Chain D: Q.36, K.37, P.39, Q.42 Ligand excluded by PLIP

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

CL.3: 4 residues within 4Å: Chain A: A.167, G.170, H.204, A.206 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: I.41, G.44, A.45 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain B: Q.36, Q.42 Ligand excluded by PLIP CL.17: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.23: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.24: 4 residues within 4Å: Chain B: T.3, L.4, L.5, N.6 Ligand excluded by PLIP CL.25: 4 residues within 4Å: Chain A: S.180 Chain B: G.179, S.180, Y.181 Ligand excluded by PLIP CL.26: 2 residues within 4Å: Chain B: F.147 Chain D: F.385 Ligand excluded by PLIP CL.32: 4 residues within 4Å: Chain C: A.167, G.170, H.204, A.206 Ligand excluded by PLIP CL.37: 3 residues within 4Å: Chain C: I.41, G.44, A.45 Ligand excluded by PLIP CL.45: 2 residues within 4Å: Chain D: Q.36, Q.42 Ligand excluded by PLIP CL.46: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.52: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.53: 4 residues within 4Å: Chain D: T.3, L.4, L.5, N.6 Ligand excluded by PLIP CL.54: 4 residues within 4Å: Chain C: S.180 Chain D: G.179, S.180, Y.181 Ligand excluded by PLIP CL.55: 2 residues within 4Å: Chain B: F.385 Chain D: F.147 Ligand excluded by PLIP

2 x F9F: 2-({[4-(TRIFLUOROMETHOXY)PHENYL]SULFONYL}AMINO)ETHYL DIHYDROGEN PHOSPHATE(Non-covalent)

F9F.4: 20 residues within 4Å: Chain A: F.22, E.49, A.59, I.64, L.100, L.127, A.129, I.153, Y.175, T.183, G.184, A.185, F.212, G.213, I.214, I.232, S.233, G.234, S.235 Chain B: P.18 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.100, A:L.100, A:Y.175, A:T.183 Hydrogen bonds: A:G.184, A:F.212, A:G.213, A:I.214, A:G.234, A:S.235 Water bridges: A:I.214 pi-Stacking: A:F.212 F9F.33: 20 residues within 4Å: Chain C: F.22, E.49, A.59, I.64, L.100, L.127, A.129, I.153, Y.175, T.183, G.184, A.185, F.212, G.213, I.214, 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.100, C:Y.175, C:T.183 Hydrogen bonds: C:Y.175, C:G.184, C:F.212, C:G.213, C:I.214, C:G.234, C:S.235 Water bridges: C:I.214 pi-Stacking: C:F.212

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

PEG.5: 6 residues within 4Å: Chain A: F.107, N.108, N.109, G.110 Chain B: R.275, V.276 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.275 PEG.34: 6 residues within 4Å: Chain C: F.107, N.108, N.109, G.110 Chain D: R.275, V.276 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.275

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

EDO.7: 5 residues within 4Å: Chain A: E.134, E.135 Chain B: T.2, P.7, M.15 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.2, A:E.135 Water bridges: B:T.3 EDO.18: 4 residues within 4Å: Chain B: Y.133, E.172, R.175, D.176 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.172, B:R.175, B:D.176 EDO.19: 2 residues within 4Å: Chain B: R.363, E.364 1 PLIP interactions: 1 interactions with chain B Water bridges: B:E.364 EDO.20: 3 residues within 4Å: Chain B: Y.8, F.9, Y.315 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Y.8 EDO.21: 6 residues within 4Å: Chain B: I.157, P.158, V.159, H.160, S.161, E.172 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.160, B:S.161, B:S.161 EDO.22: 6 residues within 4Å: Chain B: H.273, G.274, R.275, M.286, M.287, Q.288 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.274, B:Q.288 Water bridges: B:H.273, B:E.295 EDO.36: 5 residues within 4Å: Chain C: E.134, E.135 Chain D: T.2, P.7, M.15 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Water bridges: D:T.3 Hydrogen bonds: C:E.135 EDO.47: 4 residues within 4Å: Chain D: Y.133, E.172, R.175, D.176 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:E.172, D:E.172, D:R.175, D:D.176 EDO.48: 2 residues within 4Å: Chain D: R.363, E.364 1 PLIP interactions: 1 interactions with chain D Water bridges: D:E.364 EDO.49: 3 residues within 4Å: Chain D: Y.8, F.9, Y.315 1 PLIP interactions: 1 interactions with chain D Water bridges: D:Y.8 EDO.50: 6 residues within 4Å: Chain D: I.157, P.158, V.159, H.160, S.161, E.172 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:H.160, D:S.161, D:S.161 EDO.51: 6 residues within 4Å: Chain D: H.273, G.274, R.275, M.286, M.287, Q.288 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:G.274, D:Q.288 Water bridges: D:H.273, D:E.295

2 x 0JO: 2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid(Non-covalent)

0JO.9: 24 residues within 4Å: Chain B: A.85, H.86, K.87, T.110, G.111, A.112, G.113, Q.114, H.115, L.166, 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 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:A.85, B:L.166, B:A.348, B:E.350 Hydrogen bonds: B:K.87, B:G.111, B:A.112, B:G.113, B:Q.114, B:H.115, B:T.190, B:T.190, B:G.232, B:G.234, B:S.235, B:N.236, B:N.236, B:S.377 Water bridges: B:E.109, B:G.233, B:G.233, B:A.237 Salt bridges: B:H.86, B:K.87, B:K.87 pi-Stacking: B:H.86 0JO.38: 24 residues within 4Å: Chain D: A.85, H.86, K.87, T.110, G.111, A.112, G.113, Q.114, H.115, L.166, 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 26 PLIP interactions: 26 interactions with chain D Hydrophobic interactions: D:A.85, D:L.166, D:A.348, D:E.350 Hydrogen bonds: D:K.87, D:T.110, D:G.111, D:A.112, D:G.113, D:Q.114, D:H.115, D:T.190, D:G.232, D:G.234, D:S.235, D:N.236, D:N.236, D:S.377 Water bridges: D:E.109, D:G.233, D:G.233, D:A.237 Salt bridges: D:H.86, D:K.87, D:K.87 pi-Stacking: D:H.86

6 x CS: CESIUM ION(Non-covalent)

CS.27: 6 residues within 4Å: Chain B: V.231, G.232, G.268, L.304, F.306, S.308 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:G.268, B:F.306 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.14 CS.29: 7 residues within 4Å: Chain B: G.54, P.56 Chain D: G.54, P.56 Ligands: DMS.10, DMS.39, CS.58 No protein-ligand interaction detected (PLIP) CS.56: 6 residues within 4Å: Chain D: V.231, G.232, G.268, L.304, F.306, S.308 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:G.268, D:F.306 CS.57: 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.31 CS.58: 7 residues within 4Å: Chain B: G.54, P.56 Chain D: G.54, P.56 Ligands: DMS.10, CS.29, DMS.39 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hilario, E. et al., The aminoacrylate form of the beta-K167T mutant Tryptophan Synthase at 1.80 Angstrom resolution in complex with N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the enzyme alpha-site and cesium ion at the metal coordination site. To be Published

Release Date

2022-02-23

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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