SMTL ID : 6xsy.1

The external aldimine crystal structure of Salmonella typhimurium Tryptophan Synthase mutant beta-S377A with inhibitor 2-({[4-(trifluoromethoxy)phenyl]sulfonyl}amino)ethyl dihydrogen phosphate (F9F) at the alpha-site, Cesium ion at the metal coordination site, and (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-serine (KOU) at the beta-site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

hetero-1-1-mer

Ligands

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

DMS.1: 5 residues within 4Å: Chain A: I.41, H.92, P.93, T.94, I.95 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.3: 7 residues within 4Å: Chain A: L.191, P.192, L.193, Q.210, A.222, A.223, A.226 Ligand excluded by PLIP DMS.4: 5 residues within 4Å: Chain A: L.34, K.35, D.38, L.87, K.91 Ligand excluded by PLIP DMS.5: 3 residues within 4Å: Chain A: A.43, R.256, S.260 Ligand excluded by PLIP DMS.6: 2 residues within 4Å: Chain A: H.194, R.225 Ligand excluded by PLIP DMS.7: 4 residues within 4Å: Chain A: S.55, L.69, F.72 Chain B: G.162 Ligand excluded by PLIP DMS.9: 6 residues within 4Å: Chain A: M.1, L.144, N.147, I.148, A.149, R.171 Ligand excluded by PLIP DMS.16: 4 residues within 4Å: Chain B: Y.133, E.172, R.175, D.176 Ligand excluded by PLIP DMS.17: 4 residues within 4Å: Chain B: K.50, G.54, R.55, P.56 Ligand excluded by PLIP DMS.18: 5 residues within 4Å: Chain B: Q.42, F.45, A.46, L.49, M.207 Ligand excluded by PLIP DMS.19: 2 residues within 4Å: Chain B: K.99, R.100 Ligand excluded by PLIP DMS.20: 4 residues within 4Å: Chain B: I.262, G.265, H.267, H.273 Ligand excluded by PLIP DMS.21: 4 residues within 4Å: Chain B: P.56, E.211, A.214, Q.215 Ligand excluded by PLIP DMS.22: 5 residues within 4Å: Chain A: S.180 Chain B: G.179, S.180, Y.181, E.182 Ligand excluded by PLIP DMS.23: 5 residues within 4Å: Chain B: P.270, L.271, K.272, H.273, G.274 Ligand excluded by PLIP DMS.24: 5 residues within 4Å: Chain B: P.23, A.24, Q.27, Y.181, E.182 Ligand excluded by PLIP DMS.27: 2 residues within 4Å: Chain B: R.202, Q.312 Ligand excluded by PLIP DMS.28: 6 residues within 4Å: Chain B: Q.36, K.37, D.38, P.39, Q.42 Ligands: EDO.26 Ligand excluded by PLIP DMS.29: 5 residues within 4Å: Chain B: G.274, M.286, M.287, Q.288, E.295 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 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.100, A:L.127, A:Y.175, A:T.183 Hydrogen bonds: A:Y.175, A:G.184, A:F.212, A:G.213, A:G.234, A:S.235 Water bridges: A:I.214, A:I.214 pi-Stacking: A:F.212

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

EDO.10: 3 residues within 4Å: Chain A: P.217, F.258, A.261 No protein-ligand interaction detected (PLIP) EDO.11: 4 residues within 4Å: Chain A: N.12, R.15, E.16, V.224 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.12, A:E.16 Water bridges: A:N.12, A:R.15, A:G.17 EDO.25: 4 residues within 4Å: Chain B: S.143, V.146, F.147, R.150 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.147, B:R.150 Water bridges: B:S.143 EDO.26: 3 residues within 4Å: Chain B: Q.36, Q.42 Ligands: DMS.28 3 PLIP interactions: 3 interactions with chain B Water bridges: B:Q.36, B:Q.36, B:Q.42

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

CL.12: 1 residues within 4Å: Chain A: F.114 Ligand excluded by PLIP CL.13: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain A: F.107, N.108 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain A: S.221, A.265, R.267 Ligand excluded by PLIP CL.33: 2 residues within 4Å: Chain B: D.225, S.249 Ligand excluded by PLIP CL.34: 2 residues within 4Å: Chain B: K.368, E.369 Ligand excluded by PLIP CL.35: 1 residues within 4Å: Chain B: D.323 Ligand excluded by PLIP CL.36: 4 residues within 4Å: Chain B: T.3, L.4, L.5, N.6 Ligand excluded by PLIP CL.37: 1 residues within 4Å: Chain B: Y.8 Ligand excluded by PLIP

1 x KOU: (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-serine(Non-covalent)

KOU.30: 20 residues within 4Å: Chain B: H.86, K.87, T.110, G.111, A.112, G.113, Q.114, H.115, T.190, V.231, G.232, G.233, G.234, S.235, N.236, A.302, G.303, L.304, D.305, E.350 24 PLIP interactions: 24 interactions with chain B Hydrogen bonds: B:K.87, B:T.110, B:G.111, B:A.112, B:G.113, B:Q.114, B:H.115, B:G.232, B:G.233, B:G.234, B:S.235, B:N.236, B:N.236, B:D.305 Water bridges: B:T.190, B:T.190, B:G.234, B:A.237, B:E.350, B:E.350 Salt bridges: B:H.86, B:K.87, B:K.87 pi-Stacking: B:H.86

2 x CS: CESIUM ION(Non-covalent)

CS.31: 3 residues within 4Å: Chain B: T.66, T.69, T.71 No protein-ligand interaction detected (PLIP) CS.32: 6 residues within 4Å: Chain B: V.231, G.232, G.268, S.297, L.304, F.306 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:G.268, B:F.306

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hilario, E. et al., The external aldimine crystal structure of Salmonella typhimurium Tryptophan Synthase mutant beta-S377A with inhibitor 2-({[4-(trifluoromethoxy)phenyl]sulfonyl}amino)ethyl dihydrogen phosphate (F9F) at the alpha-site, Cesium ion at the metal coordination site, and (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-serine (KOU) at the beta-site. To be Published

Release Date

2021-07-21

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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