SMTL ID : 6dzo.1

Crystal structure of Salmonella typhimurium Tryptophan Synthase mutant beta-Q114A with 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 at the beta-site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.64 Å

Oligo State

hetero-2-2-mer

Ligands

2 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.17 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.100, A:L.127, A:I.153, A:Y.175, A:T.183 Hydrogen bonds: 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 F9F.28: 18 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, F.212, G.213, I.232, S.233, G.234, S.235 Chain D: P.17 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:L.100, C:L.127, C:I.153, C:Y.175, C:T.183 Hydrogen bonds: C:Y.175, C:G.184, C:F.212, C:G.213, C:G.234, C:S.235 Water bridges: C:I.214, C:I.214, C:A.236 pi-Stacking: C:F.212

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

DMS.2: 7 residues within 4Å: Chain A: V.128, S.136, F.139, R.140, P.150, I.151, F.152 Ligand excluded by PLIP DMS.3: 10 residues within 4Å: Chain A: M.1, E.2, R.3, E.119, G.122, V.123, D.124, H.146, N.147, I.148 Ligand excluded by PLIP DMS.4: 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.5: 5 residues within 4Å: Chain A: S.221, V.224, R.225, R.267, A.268 Ligand excluded by PLIP DMS.6: 5 residues within 4Å: Chain A: I.41, H.92, P.93, T.94, I.95 Ligand excluded by PLIP DMS.13: 5 residues within 4Å: Chain B: Q.41, F.44, A.45, L.48, M.206 Ligand excluded by PLIP DMS.14: 3 residues within 4Å: Chain B: I.261, H.266, H.272 Ligand excluded by PLIP DMS.15: 6 residues within 4Å: Chain B: Q.35, K.36, D.37, P.38, Q.41 Ligands: EDO.11 Ligand excluded by PLIP DMS.16: 8 residues within 4Å: Chain B: P.55, T.56, Q.214 Chain D: K.49, G.53, R.54, P.55 Ligands: DMS.43 Ligand excluded by PLIP DMS.29: 7 residues within 4Å: Chain C: V.128, S.136, F.139, R.140, P.150, I.151, F.152 Ligand excluded by PLIP DMS.30: 10 residues within 4Å: Chain C: M.1, E.2, R.3, E.119, G.122, V.123, D.124, H.146, N.147, I.148 Ligand excluded by PLIP DMS.31: 7 residues within 4Å: Chain C: L.191, P.192, L.193, Q.210, A.222, A.223, A.226 Ligand excluded by PLIP DMS.32: 5 residues within 4Å: Chain C: S.221, V.224, R.225, R.267, A.268 Ligand excluded by PLIP DMS.33: 5 residues within 4Å: Chain C: I.41, H.92, P.93, T.94, I.95 Ligand excluded by PLIP DMS.40: 5 residues within 4Å: Chain D: Q.41, F.44, A.45, L.48, M.206 Ligand excluded by PLIP DMS.41: 3 residues within 4Å: Chain D: I.261, H.266, H.272 Ligand excluded by PLIP DMS.42: 6 residues within 4Å: Chain D: Q.35, K.36, D.37, P.38, Q.41 Ligands: EDO.38 Ligand excluded by PLIP DMS.43: 8 residues within 4Å: Chain B: K.49, G.53, R.54, P.55 Chain D: P.55, T.56, Q.214 Ligands: DMS.16 Ligand excluded by PLIP

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

CL.7: 4 residues within 4Å: Chain A: A.167, G.170, H.204, A.206 Ligand excluded by PLIP CL.8: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.9: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.18: 4 residues within 4Å: Chain B: T.2, L.3, L.4, N.5 Ligand excluded by PLIP CL.19: 1 residues within 4Å: Chain B: E.10 Ligand excluded by PLIP CL.20: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.21: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.22: 1 residues within 4Å: Chain B: H.356 Ligand excluded by PLIP CL.23: 4 residues within 4Å: Chain B: S.296, Y.297, S.298, D.304 Ligand excluded by PLIP CL.24: 4 residues within 4Å: Chain B: D.217, K.218, E.219, G.220 Ligand excluded by PLIP CL.25: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.26: 4 residues within 4Å: Chain B: D.224, K.367, E.368, Q.369 Ligand excluded by PLIP CL.27: 4 residues within 4Å: Chain A: S.180 Chain B: G.178, S.179, Y.180 Ligand excluded by PLIP CL.34: 4 residues within 4Å: Chain C: A.167, G.170, H.204, A.206 Ligand excluded by PLIP CL.35: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.36: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.45: 4 residues within 4Å: Chain D: T.2, L.3, L.4, N.5 Ligand excluded by PLIP CL.46: 1 residues within 4Å: Chain D: E.10 Ligand excluded by PLIP CL.47: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.48: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.49: 1 residues within 4Å: Chain D: H.356 Ligand excluded by PLIP CL.50: 4 residues within 4Å: Chain D: S.296, Y.297, S.298, D.304 Ligand excluded by PLIP CL.51: 4 residues within 4Å: Chain D: D.217, K.218, E.219, G.220 Ligand excluded by PLIP CL.52: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.53: 4 residues within 4Å: Chain D: D.224, K.367, E.368, Q.369 Ligand excluded by PLIP CL.54: 4 residues within 4Å: Chain C: S.180 Chain D: G.178, S.179, Y.180 Ligand excluded by PLIP

4 x CS: CESIUM ION(Non-covalent)

CS.10: 3 residues within 4Å: Chain B: T.65, T.68, T.70 No protein-ligand interaction detected (PLIP) CS.12: 6 residues within 4Å: Chain B: V.230, G.231, E.255, G.267, P.269, S.307 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.255 CS.37: 3 residues within 4Å: Chain D: T.65, T.68, T.70 No protein-ligand interaction detected (PLIP) CS.39: 6 residues within 4Å: Chain D: V.230, G.231, E.255, G.267, P.269, S.307 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:E.255

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

EDO.11: 3 residues within 4Å: Chain B: Q.35, Q.41 Ligands: DMS.15 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Q.35 EDO.38: 3 residues within 4Å: Chain D: Q.35, Q.41 Ligands: DMS.42 1 PLIP interactions: 1 interactions with chain D Water bridges: D:Q.35

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

KOU.17: 24 residues within 4Å: Chain B: A.84, H.85, K.86, T.109, G.110, A.111, G.112, A.113, H.114, T.189, C.229, V.230, G.231, G.232, G.233, S.234, N.235, A.301, G.302, L.303, D.304, E.349, S.376, G.377 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:A.84 Hydrogen bonds: B:K.86, B:G.110, B:A.111, B:G.112, B:A.113, B:H.114, B:T.189, B:G.231, B:G.232, B:G.233, B:S.234, B:N.235, B:N.235, B:D.304, B:S.376 Water bridges: B:E.108, B:G.233, B:A.236, B:E.349 Salt bridges: B:H.85, B:K.86, B:K.86 pi-Stacking: B:H.85 KOU.44: 24 residues within 4Å: Chain D: A.84, H.85, K.86, T.109, G.110, A.111, G.112, A.113, H.114, T.189, C.229, V.230, G.231, G.232, G.233, S.234, N.235, A.301, G.302, L.303, D.304, E.349, S.376, G.377 26 PLIP interactions: 26 interactions with chain D Hydrophobic interactions: D:A.84 Hydrogen bonds: D:K.86, D:T.109, D:G.110, D:A.111, D:G.112, D:A.113, D:H.114, D:G.231, D:G.232, D:G.233, D:S.234, D:N.235, D:N.235, D:D.304, D:S.376 Water bridges: D:E.108, D:T.189, D:T.189, D:G.233, D:A.236, D:E.349 Salt bridges: D:H.85, D:K.86, D:K.86 pi-Stacking: D:H.85

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hilario, E. et al., Crystal structure of Salmonella typhimurium Tryptophan Synthase mutant beta-Q114A with 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 at the beta-site. To be Published

Release Date

2019-07-10

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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