SMTL ID : 4kkx.1

Crystal structure of Tryptophan Synthase from Salmonella typhimurium with 2-aminophenol quinonoid in the beta site and the F6 inhibitor in the alpha site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

hetero-2-2-mer

Ligands

2 x F6F: 2-{[4-(TRIFLUOROMETHOXY)BENZOYL]AMINO}ETHYL DIHYDROGEN PHOSPHATE(Non-covalent)

F6F.1: 16 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, G.234, S.235 Chain B: P.18 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.100, 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:D.60, A:I.214, A:I.214, A:A.236 pi-Stacking: A:F.212 F6F.20: 16 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, G.234, S.235 Chain D: P.18 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:L.100, 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:D.60, C:I.214, C:I.214, C:A.236 pi-Stacking: C:F.212

6 x NA: SODIUM ION(Non-functional Binders)

NA.2: 7 residues within 4Å: Chain A: N.104, F.107, N.108 Chain B: R.275, V.276, G.277, Q.288 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.104, A:N.104, B:R.275, B:Q.288 NA.7: 5 residues within 4Å: Chain B: G.232, G.268, P.270, F.306, S.308 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.306, B:S.308 NA.8: 7 residues within 4Å: Chain B: C.230, V.231, G.234, S.235, N.236, A.237 Ligands: AQ3.6 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:C.230, B:G.234, B:N.236, B:A.237 NA.21: 7 residues within 4Å: Chain C: N.104, F.107, N.108 Chain D: R.275, V.276, G.277, Q.288 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:R.275, D:Q.288, C:N.104, C:N.104 NA.26: 5 residues within 4Å: Chain D: G.232, G.268, P.270, F.306, S.308 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.308, D:S.308 NA.27: 7 residues within 4Å: Chain D: C.230, V.231, G.234, S.235, N.236, A.237 Ligands: AQ3.25 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:G.234, D:G.234, D:N.236, D:A.237

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

EDO.3: 4 residues within 4Å: Chain A: R.164, Q.165, S.168, Y.169 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain B: P.56, Q.215, K.219 Chain D: K.50 Ligands: PGE.18 Ligand excluded by PLIP EDO.10: 3 residues within 4Å: Chain B: N.6, Y.8, G.10 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain B: T.66, T.69, R.70, T.71, T.72 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain B: H.273, V.325, S.326 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain A: E.134, L.162 Chain B: Q.19, M.22, P.23, N.26 Ligand excluded by PLIP EDO.14: 1 residues within 4Å: Chain B: K.272 Ligand excluded by PLIP EDO.15: 2 residues within 4Å: Chain B: R.275, V.276 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain B: T.3, L.4, L.5, N.6 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain B: E.266, E.296, S.297, Y.298 Ligand excluded by PLIP EDO.22: 4 residues within 4Å: Chain C: R.164, Q.165, S.168, Y.169 Ligand excluded by PLIP EDO.28: 5 residues within 4Å: Chain B: K.50 Chain D: P.56, Q.215, K.219 Ligands: PGE.37 Ligand excluded by PLIP EDO.29: 3 residues within 4Å: Chain D: N.6, Y.8, G.10 Ligand excluded by PLIP EDO.30: 5 residues within 4Å: Chain D: T.66, T.69, R.70, T.71, T.72 Ligand excluded by PLIP EDO.31: 3 residues within 4Å: Chain D: H.273, V.325, S.326 Ligand excluded by PLIP EDO.32: 6 residues within 4Å: Chain C: E.134, L.162 Chain D: Q.19, M.22, P.23, N.26 Ligand excluded by PLIP EDO.33: 1 residues within 4Å: Chain D: K.272 Ligand excluded by PLIP EDO.34: 2 residues within 4Å: Chain D: R.275, V.276 Ligand excluded by PLIP EDO.35: 4 residues within 4Å: Chain D: T.3, L.4, L.5, N.6 Ligand excluded by PLIP EDO.36: 4 residues within 4Å: Chain D: E.266, E.296, S.297, Y.298 Ligand excluded by PLIP

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

PEG.4: 8 residues within 4Å: Chain A: G.61, P.62, R.179, G.181, V.182, T.183, G.184, N.187 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.182, A:N.187 Water bridges: A:E.186, A:E.186, A:N.187 PEG.5: 5 residues within 4Å: Chain A: N.12, R.15, E.16, G.17, V.224 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.12 PEG.23: 8 residues within 4Å: Chain C: G.61, P.62, R.179, G.181, V.182, T.183, G.184, N.187 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:V.182, C:N.187 Water bridges: C:N.187 PEG.24: 5 residues within 4Å: Chain C: N.12, R.15, E.16, G.17, V.224 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.12

2 x AQ3: N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-3-[(2-hydroxyphenyl)amino]-D-alanine(Non-covalent)

AQ3.6: 28 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 Ligands: NA.8 27 PLIP interactions: 27 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:E.109, B:G.111, B:A.112, B:G.113, B:Q.114, B:H.115, B:T.190, B:G.232, B:G.233, B:G.234, B:S.235, B:N.236, B:N.236, B:S.377 Salt bridges: B:H.86, B:K.87, B:K.87 pi-Stacking: B:H.86, B:F.306 AQ3.25: 28 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 Ligands: NA.27 28 PLIP interactions: 28 interactions with chain D Hydrophobic interactions: D:A.85, D:L.166, D:T.190, D:A.348, D:E.350 Hydrogen bonds: D:H.86, D:K.87, D:K.87, D:E.109, D:T.110, 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 Salt bridges: D:H.86, D:K.87, D:K.87 pi-Stacking: D:H.86, D:F.306

4 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.18: 7 residues within 4Å: Chain B: P.56, E.210, E.211, A.214, Q.215, D.218 Ligands: EDO.9 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.210 Water bridges: B:A.214, B:D.218 PGE.19: 11 residues within 4Å: Chain B: L.59, T.60, K.61, Q.63, Y.74, K.219, E.343 Chain D: D.47, N.51, Y.52, L.125 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.61, B:Q.63, B:E.343 PGE.37: 7 residues within 4Å: Chain D: P.56, E.210, E.211, A.214, Q.215, D.218 Ligands: EDO.28 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.210 Water bridges: D:A.214, D:D.218 PGE.38: 11 residues within 4Å: Chain B: D.47, N.51, Y.52, L.125 Chain D: L.59, T.60, K.61, Q.63, Y.74, K.219, E.343 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:K.61, D:Q.63, D:E.343, D:E.343

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Niks, D. et al., Allostery and substrate channeling in the tryptophan synthase bienzyme complex: evidence for two subunit conformations and four quaternary states. Biochemistry (2013)

Release Date

2014-01-01

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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