SMTL ID : 6xe3.1

Salmonella typhimurium Tryptophan Synthase beta-S377A mutant in complex with inhibitor F9 at the enzyme alpha-site, cesium ion at the metal coordination site and carbanion III E(C3) at the enzyme beta-site.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

hetero-1-1-mer

Ligands

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

F9F.1: 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 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.100, A:L.127, A:I.153, 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, A:A.236 pi-Stacking: A:F.212

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

EDO.2: 5 residues within 4Å: Chain A: I.41, G.44, A.45, D.46, K.263 2 PLIP interactions: 2 interactions with chain A Water bridges: A:I.41, A:A.45 EDO.5: 5 residues within 4Å: Chain A: F.107, N.108, G.110 Chain B: R.275, V.276 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.275, A:N.108, A:G.110 Water bridges: B:Q.288 EDO.15: 1 residues within 4Å: Chain B: E.210 3 PLIP interactions: 3 interactions with chain B Water bridges: B:E.210, B:D.243, B:D.243 EDO.16: 4 residues within 4Å: Chain B: T.248, S.249, G.251 Ligands: CS.23 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.321 EDO.17: 2 residues within 4Å: Chain B: Q.63, N.64 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.64 EDO.18: 2 residues within 4Å: Chain B: Q.36, Q.42 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Q.36 EDO.20: 1 residues within 4Å: Chain B: D.218 1 PLIP interactions: 1 interactions with chain B Water bridges: B:D.218 EDO.43: 6 residues within 4Å: Chain B: I.65, T.338, H.342, L.359, M.362, R.363 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.342, B:R.363 Water bridges: B:R.363

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

DMS.3: 6 residues within 4Å: Chain A: N.12, R.15, E.16, G.17, V.224, A.228 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.12 DMS.4: 7 residues within 4Å: Chain A: L.191, P.192, L.193, H.194, Q.210, A.222, A.226 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.193, A:H.194 DMS.8: 9 residues within 4Å: Chain A: M.1, R.3, E.119, G.122, V.123, D.124, H.146, N.147, I.148 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.1 Water bridges: A:R.3 Salt bridges: A:D.124 DMS.9: 5 residues within 4Å: Chain A: I.41, H.92, P.93, T.94, I.95 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.94, A:I.95 DMS.10: 8 residues within 4Å: Chain A: V.128, V.131, S.136, F.139, R.140, P.150, I.151, F.152 No protein-ligand interaction detected (PLIP) DMS.11: 3 residues within 4Å: Chain A: F.82, F.114, R.117 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.79 DMS.13: 3 residues within 4Å: Chain B: S.143, P.144, F.147 No protein-ligand interaction detected (PLIP) DMS.14: 2 residues within 4Å: Chain B: R.363, E.364 No protein-ligand interaction detected (PLIP) DMS.19: 3 residues within 4Å: Chain B: H.357, M.361, E.364 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:E.364 DMS.38: 4 residues within 4Å: Chain B: K.50, G.54, R.55, P.56 No protein-ligand interaction detected (PLIP) DMS.39: 5 residues within 4Å: Chain B: Q.42, F.45, A.46, L.49, M.207 No protein-ligand interaction detected (PLIP) DMS.40: 4 residues within 4Å: Chain B: I.262, G.265, H.267, H.273 No protein-ligand interaction detected (PLIP) DMS.41: 4 residues within 4Å: Chain B: P.56, E.211, A.214, Q.215 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.215 DMS.42: 2 residues within 4Å: Chain B: E.331, K.360 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:E.331

4 x CS: CESIUM ION(Non-covalent)

CS.6: 4 residues within 4Å: Chain A: A.167, G.170, H.204, A.206 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:A.167 CS.21: 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 CS.22: 3 residues within 4Å: Chain B: T.66, T.69, T.71 No protein-ligand interaction detected (PLIP) CS.23: 3 residues within 4Å: Chain B: D.225, S.249 Ligands: EDO.16 No protein-ligand interaction detected (PLIP)

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

CL.7: 1 residues within 4Å: Chain A: E.186 Ligand excluded by PLIP CL.24: 2 residues within 4Å: Chain B: Q.36, K.37 Ligand excluded by PLIP CL.25: 2 residues within 4Å: Chain B: F.147, R.150 Ligand excluded by PLIP CL.26: 2 residues within 4Å: Chain B: K.368, E.369 Ligand excluded by PLIP CL.27: 4 residues within 4Å: Chain B: G.10, E.11, F.12, S.318 Ligand excluded by PLIP CL.28: 4 residues within 4Å: Chain B: T.3, L.4, L.5, N.6 Ligand excluded by PLIP CL.29: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.30: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.31: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.32: 1 residues within 4Å: Chain B: R.321 Ligand excluded by PLIP CL.33: 1 residues within 4Å: Chain B: D.176 Ligand excluded by PLIP CL.34: 1 residues within 4Å: Chain B: D.323 Ligand excluded by PLIP CL.35: 1 residues within 4Å: Chain B: R.341 Ligand excluded by PLIP CL.36: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.37: 1 residues within 4Å: Chain B: Q.293 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: 26 residues within 4Å: Chain B: A.85, H.86, K.87, E.109, T.110, G.111, A.112, G.113, Q.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, E.350, A.377, G.378 29 PLIP interactions: 29 interactions with chain B Hydrophobic interactions: B:A.85, B:L.166, B:T.190, B:F.306, B:E.350 Hydrogen bonds: B:K.87, B:K.87, B:E.109, 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 Water bridges: B:G.234, B:A.237, B:E.350, B:K.382 Salt bridges: B:H.86, B:K.87, B:K.87 pi-Stacking: B:H.86, B:F.306

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hilario, E. et al., Salmonella typhimurium Tryptophan Synthase beta-S377A mutant in complex with inhibitor F9 at the enzyme alpha-site, cesium ion at the metal coordination site and carbanion III E(C3) at the enzyme beta-site. To be Published

Release Date

2021-03-10

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

Related Entries With Identical Sequence