SMTL ID : 7kbn.1

1.60 Angstrom resolution crystal structure of the beta-Q114A mutant of Tryptophan Synthase in complex with N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the enzyme alpha-site, cesium ion at the metal coordination site, and 2-aminophenol quinonoid at the enzyme beta site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

hetero-1-1-mer

Ligands

19 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: 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.7: 6 residues within 4Å: Chain A: M.1, L.144, N.147, I.148, A.149, R.171 Ligand excluded by PLIP DMS.8: 7 residues within 4Å: Chain A: A.167, S.168, G.170, R.171, H.204, A.205, A.206 Ligand excluded by PLIP DMS.20: 4 residues within 4Å: Chain B: D.218, K.219, E.220, G.221 Ligand excluded by PLIP DMS.21: 4 residues within 4Å: Chain B: P.56, T.57, A.58, Q.215 Ligand excluded by PLIP DMS.22: 5 residues within 4Å: Chain B: Q.42, F.45, A.46, L.49, M.207 Ligand excluded by PLIP DMS.23: 2 residues within 4Å: Chain B: Y.8, G.10 Ligand excluded by PLIP DMS.24: 5 residues within 4Å: Chain A: S.180 Chain B: G.179, S.180, Y.181, E.182 Ligand excluded by PLIP DMS.25: 4 residues within 4Å: Chain B: Y.133, E.172, R.175, D.176 Ligand excluded by PLIP DMS.26: 6 residues within 4Å: Chain B: I.262, G.265, H.267, H.273 Ligands: EDO.19, DMS.34 Ligand excluded by PLIP DMS.27: 2 residues within 4Å: Chain B: T.328, E.331 Ligand excluded by PLIP DMS.28: 3 residues within 4Å: Chain B: L.271, N.317 Ligands: EDO.19 Ligand excluded by PLIP DMS.29: 3 residues within 4Å: Chain B: Q.36, Q.42 Ligands: CL.37 Ligand excluded by PLIP DMS.30: 4 residues within 4Å: Chain B: N.64, I.65, T.338, H.342 Ligand excluded by PLIP DMS.31: 6 residues within 4Å: Chain B: P.23, A.24, Q.27, K.103, Y.181, E.182 Ligand excluded by PLIP DMS.32: 4 residues within 4Å: Chain B: P.56, E.211, A.214, Q.215 Ligand excluded by PLIP DMS.33: 2 residues within 4Å: Chain B: R.150, L.151 Ligand excluded by PLIP DMS.34: 3 residues within 4Å: Chain B: E.263, T.264 Ligands: DMS.26 Ligand excluded by PLIP

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

F9F.3: 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 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.100, A:L.100, A:L.127, A:Y.175, A:T.183 Hydrogen bonds: A:Y.175, A:R.179, A:G.184, A:F.212, A:G.213, A:G.234, A:S.235 Water bridges: A:F.212, A:I.214 pi-Stacking: A:F.212

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

EDO.4: 4 residues within 4Å: Chain A: N.108, N.109 Chain B: R.275, A.290 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.108 EDO.5: 4 residues within 4Å: Chain A: F.82, A.113, F.114, R.117 4 PLIP interactions: 4 interactions with chain A Water bridges: A:L.105, A:L.105, A:N.108, A:N.109 EDO.6: 7 residues within 4Å: Chain A: P.155, N.157, A.158, L.162 Chain B: Q.19, M.22, P.23 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.19, A:N.157 EDO.16: 6 residues within 4Å: Chain B: H.273, G.274, R.275, M.286, M.287, Q.288 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:M.286, B:Q.288 EDO.17: 6 residues within 4Å: Chain B: T.248, S.249, V.250, G.251, R.321 Ligands: CL.36 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.321 Water bridges: B:R.321 EDO.18: 7 residues within 4Å: Chain B: Y.133, 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:E.172 Water bridges: B:P.158 EDO.19: 5 residues within 4Å: Chain B: K.272, H.273, G.274 Ligands: DMS.26, DMS.28 No protein-ligand interaction detected (PLIP)

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

CL.9: 3 residues within 4Å: Chain A: S.180, G.181, N.187 Ligand excluded by PLIP CL.10: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain A: N.12, E.16 Ligand excluded by PLIP CL.35: 2 residues within 4Å: Chain A: P.57 Chain B: R.175 Ligand excluded by PLIP CL.36: 3 residues within 4Å: Chain B: D.225, S.249 Ligands: EDO.17 Ligand excluded by PLIP CL.37: 3 residues within 4Å: Chain B: Q.36, K.37 Ligands: DMS.29 Ligand excluded by PLIP CL.38: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

1 x 1D0: (2E)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)imino]-3-[(2-hydroxyphenyl)amino]propanoic acid(Non-covalent)

1D0.12: 27 residues within 4Å: Chain B: A.85, H.86, K.87, E.109, T.110, G.111, A.112, G.113, A.114, H.115, L.166, G.189, T.190, C.230, V.231, G.232, G.233, G.234, S.235, N.236, G.303, L.304, F.306, A.348, E.350, S.377, G.378 30 PLIP interactions: 30 interactions with chain B Hydrophobic interactions: B:A.85, B:L.166, B:T.190, B:A.348, B:E.350 Hydrogen bonds: B:H.86, B:K.87, B:K.87, B:E.109, B:T.110, B:G.111, B:G.113, B:A.114, B:H.115, B:T.190, 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:G.234, B:A.237 Salt bridges: B:H.86, B:K.87, B:K.87 pi-Stacking: B:H.86, B:F.306

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

PEG.13: 4 residues within 4Å: Chain B: T.60, K.61, C.62, E.343 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.61, B:E.343, B:E.343 Water bridges: B:L.59, B:Q.63 PEG.14: 6 residues within 4Å: Chain B: N.6, Y.8, F.9, G.10, Y.315 Ligands: PEG.15 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.6, B:G.10 Water bridges: B:Q.312, B:Y.315 PEG.15: 6 residues within 4Å: Chain B: R.202, R.206, A.242, I.245, Q.312 Ligands: PEG.14 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.206, B:A.242, B:Q.312 Water bridges: B:I.245

1 x 2AF: 2-AMINOPHENOL(Non-covalent)

2AF.39: 5 residues within 4Å: Chain B: T.3, L.4, L.5, N.6, P.7 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.6, B:N.6 Water bridges: B:T.3, B:N.6

2 x CS: CESIUM ION(Non-covalent)

CS.40: 3 residues within 4Å: Chain B: T.66, T.69, T.71 No protein-ligand interaction detected (PLIP) CS.41: 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.232, B:F.306

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hilario, E. et al., 1.60 Angstrom resolution crystal structure of the beta-Q114A mutant of Tryptophan Synthase in complex with N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the enzyme alpha-site, cesium ion at the metal coordination site, and 2-aminophenol quinonoid at the enzyme beta site. To be Published

Release Date

2021-10-13

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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