SMTL ID : 6duc.1

Crystal structure of mutant beta-K167T tryptophan synthase in complex with inhibitor N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the alpha-site, cesium ion at the metal coordination site, and 2-aminophenol quinonoid (1D0) at the beta-site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.79 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.18 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:A.59, A:L.100, A:L.100, 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 F9F.27: 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.18 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:A.59, C:L.100, C:L.100, C:Y.175, C:T.183 Hydrogen bonds: 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

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

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 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.3 Water bridges: A:M.1, A:R.3 Salt bridges: A:D.124 DMS.7: 1 residues within 4Å: Chain B: E.331 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:E.331 DMS.9: 5 residues within 4Å: Chain B: Q.42, F.45, A.46, L.49, M.207 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.46 DMS.10: 11 residues within 4Å: Chain B: K.50, G.54, R.55, P.56 Chain D: P.56, T.57, A.58, Q.215 Ligands: CS.17, DMS.36, CS.43 No protein-ligand interaction detected (PLIP) DMS.11: 5 residues within 4Å: Chain A: S.180 Chain B: G.179, S.180, Y.181, E.182 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Salt bridges: B:E.182 pi-Cation interactions: B:Y.181 Hydrogen bonds: A:S.180 DMS.14: 2 residues within 4Å: Chain B: R.363, E.364 No protein-ligand interaction detected (PLIP) DMS.28: 9 residues within 4Å: Chain C: M.1, R.3, E.119, G.122, V.123, D.124, H.146, N.147, I.148 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.3 Water bridges: C:R.3, C:D.124 Salt bridges: C:D.124 DMS.33: 1 residues within 4Å: Chain D: E.331 2 PLIP interactions: 2 interactions with chain D Water bridges: D:E.331 Salt bridges: D:E.331 DMS.35: 5 residues within 4Å: Chain D: Q.42, F.45, A.46, L.49, M.207 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:A.46 DMS.36: 11 residues within 4Å: Chain B: P.56, T.57, A.58, Q.215 Chain D: K.50, G.54, R.55, P.56 Ligands: DMS.10, CS.17, CS.43 No protein-ligand interaction detected (PLIP) DMS.37: 5 residues within 4Å: Chain C: S.180 Chain D: G.179, S.180, Y.181, E.182 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Salt bridges: D:E.182 pi-Cation interactions: D:Y.181 Hydrogen bonds: C:S.180 DMS.40: 2 residues within 4Å: Chain D: R.363, E.364 No protein-ligand interaction detected (PLIP)

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

EDO.3: 2 residues within 4Å: Chain A: A.113, A.116 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.117 Water bridges: A:D.112 EDO.12: 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.13: 7 residues within 4Å: Chain B: T.60, K.61, Q.63, E.343 Chain D: L.48, Y.52, L.125 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:Q.63, B:E.343, B:E.343 Water bridges: B:K.61, D:N.51 EDO.29: 2 residues within 4Å: Chain C: A.113, A.116 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.117 Water bridges: C:D.112, C:D.112 EDO.38: 6 residues within 4Å: Chain D: H.273, G.274, R.275, M.286, M.287, Q.288 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:M.286, D:Q.288 EDO.39: 7 residues within 4Å: Chain B: L.48, Y.52, L.125 Chain D: T.60, K.61, Q.63, E.343 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:Q.63, D:E.343 Water bridges: D:K.61, B:N.51

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

CL.4: 3 residues within 4Å: Chain A: I.41, G.44, A.45 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: A.167, G.170, H.204 Ligand excluded by PLIP CL.18: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.19: 2 residues within 4Å: Chain B: E.263, T.264 Ligand excluded by PLIP CL.20: 3 residues within 4Å: Chain B: E.367, K.368, E.369 Ligand excluded by PLIP CL.21: 3 residues within 4Å: Chain B: K.219, E.220, G.221 Ligand excluded by PLIP CL.22: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.23: 2 residues within 4Å: Chain B: R.275, A.290 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: Q.36, Q.42 Ligand excluded by PLIP CL.26: 2 residues within 4Å: Chain B: V.325, S.326 Ligand excluded by PLIP CL.30: 3 residues within 4Å: Chain C: I.41, G.44, A.45 Ligand excluded by PLIP CL.31: 3 residues within 4Å: Chain C: A.167, G.170, H.204 Ligand excluded by PLIP CL.44: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.45: 2 residues within 4Å: Chain D: E.263, T.264 Ligand excluded by PLIP CL.46: 3 residues within 4Å: Chain D: E.367, K.368, E.369 Ligand excluded by PLIP CL.47: 3 residues within 4Å: Chain D: K.219, E.220, G.221 Ligand excluded by PLIP CL.48: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.49: 2 residues within 4Å: Chain D: R.275, A.290 Ligand excluded by PLIP CL.50: 2 residues within 4Å: Chain D: Q.36, K.37 Ligand excluded by PLIP CL.51: 2 residues within 4Å: Chain D: Q.36, Q.42 Ligand excluded by PLIP CL.52: 2 residues within 4Å: Chain D: V.325, S.326 Ligand excluded by PLIP

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

1D0.6: 27 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, A.348, E.350, S.377, G.378 28 PLIP interactions: 28 interactions with chain B Hydrophobic interactions: B:A.85, B:L.166, B:T.190, B:A.348, 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, 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 1D0.32: 27 residues within 4Å: Chain D: 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, A.348, E.350, S.377, G.378 29 PLIP interactions: 29 interactions with chain D Hydrophobic interactions: D:A.85, D:L.166, D:T.190, D:A.348, D:E.350 Hydrogen bonds: D:K.87, D:K.87, D:E.109, D:E.109, D:G.111, D:A.112, D:G.113, D:Q.114, D:H.115, D:T.190, D:G.232, D:G.233, D:G.234, D:S.235, D:N.236, D:N.236, D:S.377 Water bridges: D:G.234, D:A.237 Salt bridges: D:H.86, D:K.87, D:K.87 pi-Stacking: D:H.86, D:F.306

2 x 2AP: 2-AMINOPYRIDINE(Non-covalent)

2AP.8: 4 residues within 4Å: Chain B: T.3, L.4, L.5, N.6 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.6 Water bridges: B:N.6 2AP.34: 4 residues within 4Å: Chain D: T.3, L.4, L.5, N.6 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.6 Water bridges: D:N.6

6 x CS: CESIUM ION(Non-covalent)

CS.15: 6 residues within 4Å: Chain B: V.231, G.232, G.268, L.304, F.306, S.308 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:G.232, B:G.268, B:F.306 CS.16: 3 residues within 4Å: Chain B: T.66, T.69, T.71 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.71 CS.17: 7 residues within 4Å: Chain B: G.54, P.56 Chain D: G.54, P.56 Ligands: DMS.10, DMS.36, CS.43 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Metal complexes: B:P.56, D:P.56 CS.41: 6 residues within 4Å: Chain D: V.231, G.232, G.268, L.304, F.306, S.308 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:G.232, D:G.268, D:F.306 CS.42: 3 residues within 4Å: Chain D: T.66, T.69, T.71 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.71 CS.43: 7 residues within 4Å: Chain B: G.54, P.56 Chain D: G.54, P.56 Ligands: DMS.10, CS.17, DMS.36 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Metal complexes: B:P.56, D:P.56

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hilario, E. et al., Tryptophan synthase Q114A mutant in complex with inhibitor N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the alpha-site, aminoacrylate (P1T) at the beta site, and cesium ion at the metal coordination site. To be Published

Release Date

2019-06-26

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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