SMTL ID : 7ka1.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

hetero-1-1-mer

Ligands

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

DMS.1: 3 residues within 4Å: Chain A: S.55, F.72 Chain B: Q.293 Ligand excluded by PLIP DMS.2: 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.3: 3 residues within 4Å: Chain A: F.82, F.114, R.117 Ligand excluded by PLIP DMS.4: 6 residues within 4Å: Chain A: S.221, V.224, R.225, A.265, R.267, A.268 Ligand excluded by PLIP DMS.5: 8 residues within 4Å: Chain A: Y.115, V.128, V.131, F.139, R.140, P.150, I.151, F.152 Ligand excluded by PLIP DMS.13: 7 residues within 4Å: Chain A: S.180 Chain B: G.179, S.180, Y.181, E.182 Ligands: EDO.9, PEG.36 Ligand excluded by PLIP DMS.14: 4 residues within 4Å: Chain B: P.56, T.57, A.58, Q.215 Ligand excluded by PLIP DMS.15: 3 residues within 4Å: Chain B: K.137, E.266, Y.298 Ligand excluded by PLIP DMS.16: 4 residues within 4Å: Chain B: Q.42, F.45, A.46, L.49 Ligand excluded by PLIP DMS.17: 9 residues within 4Å: Chain B: A.120, S.123, A.124, L.128, K.129, C.130, M.152, G.153, A.154 Ligand excluded by PLIP DMS.18: 4 residues within 4Å: Chain B: N.64, I.65, T.338, H.342 Ligand excluded by PLIP DMS.19: 1 residues within 4Å: Chain B: E.331 Ligand excluded by PLIP DMS.20: 3 residues within 4Å: Chain B: I.262, H.267, H.273 Ligand excluded by PLIP DMS.21: 2 residues within 4Å: Chain B: Y.8, G.10 Ligand excluded by PLIP DMS.22: 3 residues within 4Å: Chain B: V.146, F.147, R.150 Ligand excluded by PLIP DMS.23: 3 residues within 4Å: Chain B: Q.36, K.37, Q.42 Ligand excluded by PLIP

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

CL.6: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain A: A.167, G.170, H.204, A.206 Ligand excluded by PLIP CL.24: 2 residues within 4Å: Chain B: Q.36, Q.42 Ligand excluded by PLIP CL.25: 1 residues within 4Å: Chain B: G.153 Ligand excluded by PLIP CL.26: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

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

F9F.8: 18 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, 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.127, A:Y.175, A:T.183 Hydrogen bonds: A:R.179, A:G.184, A:F.212, A:G.213, A:I.214, A:G.234, A:S.235 Water bridges: A:I.214, A:I.214, A:A.236 pi-Stacking: A:F.212

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

EDO.9: 6 residues within 4Å: Chain A: R.179, S.180, G.181, N.187 Chain B: G.179 Ligands: DMS.13 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.179, A:S.180, A:N.187 Water bridges: A:S.180 EDO.27: 3 residues within 4Å: Chain B: G.265, E.295, E.296 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.265, B:E.296 Water bridges: B:I.294 EDO.28: 3 residues within 4Å: Chain B: E.210, E.211, A.214 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.210 EDO.29: 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.30: 2 residues within 4Å: Chain B: R.363, E.364 2 PLIP interactions: 2 interactions with chain B Water bridges: B:K.360, B:E.364 EDO.31: 4 residues within 4Å: Chain B: N.6, Y.8, F.9, Y.315 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.6 Water bridges: B:G.10 EDO.32: 5 residues within 4Å: Chain B: P.158, V.159, H.160, S.161, E.172 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.160, B:S.161 EDO.33: 6 residues within 4Å: Chain B: H.273, G.274, R.275, M.286, M.287, Q.288 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.288 Water bridges: B:H.273, B:G.274, B:Q.288, B:E.295

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

0JO.10: 24 residues within 4Å: Chain B: A.85, H.86, K.87, T.110, G.111, A.112, G.113, A.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:A.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

2 x CS: CESIUM ION(Non-covalent)

CS.11: 6 residues within 4Å: Chain B: V.231, G.232, G.268, L.304, F.306, S.308 No protein-ligand interaction detected (PLIP) CS.12: 3 residues within 4Å: Chain B: T.66, T.69, T.71 No protein-ligand interaction detected (PLIP)

1 x SER: SERINE(Non-covalent)

SER.34: 9 residues within 4Å: Chain A: S.55, D.56, P.57, Q.65, L.69 Chain B: S.161, G.162, N.171, R.175 8 PLIP interactions: 1 Ligand-Ligand interactions, 6 interactions with chain B, 1 interactions with chain A Water bridges: S.34, B:G.162, B:K.167, B:D.168, B:E.172 Hydrogen bonds: B:N.171, A:D.56 Salt bridges: B:R.175

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

PEG.35: 3 residues within 4Å: Chain B: T.60, K.61, E.343 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.61 Water bridges: B:L.59 PEG.36: 5 residues within 4Å: Chain B: G.179, S.180, E.182, T.183 Ligands: DMS.13 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.182, B:T.183 Water bridges: B:R.131, B:D.176, B:D.176

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 Tryptophan Synthase in complex with inhibitor N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the alpha-site, aminoacrylate at the beta site, and cesium ion at the metal coordination site. To be Published

Release Date

2021-09-29

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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