SMTL ID : 6xt0.1

Salmonella typhimurium tryptophan synthase complexed with dioxindolyl-L-alanine and D-glycerol-3-phosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.37 Å

Oligo State

hetero-2-2-mer

Ligands

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

DMS.1: 6 residues within 4Å: Chain A: P.78, F.82, N.109, A.113, F.114, R.117 Ligand excluded by PLIP DMS.2: 10 residues within 4Å: Chain A: S.178, G.189, A.190, L.191, P.192, L.193, Q.210, A.222, A.223, A.226 Ligand excluded by PLIP DMS.7: 6 residues within 4Å: Chain B: S.143, P.144, F.147 Chain D: I.384, F.385, H.388 Ligand excluded by PLIP DMS.8: 5 residues within 4Å: Chain B: T.3, L.4, L.5, N.6, P.7 Ligand excluded by PLIP DMS.9: 3 residues within 4Å: Chain B: Y.8, G.10, E.11 Ligand excluded by PLIP DMS.10: 5 residues within 4Å: Chain A: V.182 Chain B: Y.133, E.172, R.175, D.176 Ligand excluded by PLIP DMS.11: 4 residues within 4Å: Chain B: P.56, E.211, A.214, Q.215 Ligand excluded by PLIP DMS.12: 6 residues within 4Å: Chain A: S.180 Chain B: G.179, S.180, Y.181, E.182, T.183 Ligand excluded by PLIP DMS.13: 5 residues within 4Å: Chain B: L.5, F.32, V.33, Q.36, E.203 Ligand excluded by PLIP DMS.14: 5 residues within 4Å: Chain B: N.64, I.65, A.67, T.338, H.342 Ligand excluded by PLIP DMS.15: 5 residues within 4Å: Chain B: Q.42, F.45, A.46, L.49, M.207 Ligand excluded by PLIP DMS.16: 3 residues within 4Å: Chain B: H.260, E.266, Y.298 Ligand excluded by PLIP DMS.17: 5 residues within 4Å: Chain B: Q.36, K.37, D.38, P.39, Q.42 Ligand excluded by PLIP DMS.18: 4 residues within 4Å: Chain B: D.218, K.219, E.220, G.221 Ligand excluded by PLIP DMS.19: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP DMS.20: 6 residues within 4Å: Chain C: P.78, F.82, N.109, A.113, F.114, R.117 Ligand excluded by PLIP DMS.21: 10 residues within 4Å: Chain C: S.178, G.189, A.190, L.191, P.192, L.193, Q.210, A.222, A.223, A.226 Ligand excluded by PLIP DMS.26: 6 residues within 4Å: Chain B: I.384, F.385, H.388 Chain D: S.143, P.144, F.147 Ligand excluded by PLIP DMS.27: 5 residues within 4Å: Chain D: T.3, L.4, L.5, N.6, P.7 Ligand excluded by PLIP DMS.28: 3 residues within 4Å: Chain D: Y.8, G.10, E.11 Ligand excluded by PLIP DMS.29: 5 residues within 4Å: Chain C: V.182 Chain D: Y.133, E.172, R.175, D.176 Ligand excluded by PLIP DMS.30: 4 residues within 4Å: Chain D: P.56, E.211, A.214, Q.215 Ligand excluded by PLIP DMS.31: 6 residues within 4Å: Chain C: S.180 Chain D: G.179, S.180, Y.181, E.182, T.183 Ligand excluded by PLIP DMS.32: 5 residues within 4Å: Chain D: L.5, F.32, V.33, Q.36, E.203 Ligand excluded by PLIP DMS.33: 5 residues within 4Å: Chain D: N.64, I.65, A.67, T.338, H.342 Ligand excluded by PLIP DMS.34: 5 residues within 4Å: Chain D: Q.42, F.45, A.46, L.49, M.207 Ligand excluded by PLIP DMS.35: 3 residues within 4Å: Chain D: H.260, E.266, Y.298 Ligand excluded by PLIP DMS.36: 5 residues within 4Å: Chain D: Q.36, K.37, D.38, P.39, Q.42 Ligand excluded by PLIP DMS.37: 4 residues within 4Å: Chain D: D.218, K.219, E.220, G.221 Ligand excluded by PLIP DMS.38: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

2 x 1GP: SN-GLYCEROL-1-PHOSPHATE(Non-covalent)

1GP.3: 16 residues within 4Å: Chain A: F.22, E.49, I.64, L.100, Y.175, R.179, T.183, G.184, G.211, F.212, G.213, I.214, I.232, S.233, G.234, S.235 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:Y.175, A:G.184, A:F.212, A:G.213, A:G.234, A:S.235, A:S.235 Water bridges: A:I.214, A:I.214, A:S.233 1GP.22: 16 residues within 4Å: Chain C: F.22, E.49, I.64, L.100, Y.175, R.179, T.183, G.184, G.211, F.212, G.213, I.214, I.232, S.233, G.234, S.235 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:Y.175, C:G.184, C:F.212, C:G.213, C:G.234, C:S.235, C:S.235 Water bridges: C:I.214, C:I.214, C:S.233

4 x X9D: 4-[(E)-({1-carboxy-2-[(3R)-3-hydroxy-2-oxo-2,3-dihydro-1H-indol-3-yl]ethan-1-id-1-yl}iminio)methyl]-2-methyl-5-[(phosphonooxy)methyl]pyridin-1-ium-3-olate(Non-covalent)

X9D.4: 32 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, G.116, L.166, C.170, 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.351, S.377, G.378, K.382 Ligands: VE4.5 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:E.109, B:E.109, B:T.110, 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:S.235, B:S.235, B:N.236, B:N.236, B:S.377 Water bridges: B:A.237 Salt bridges: B:H.86, B:K.87 pi-Stacking: B:H.86, B:F.306 X9D.5: 33 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, C.170, G.189, T.190, A.191, C.230, V.231, G.232, G.233, G.234, S.235, N.236, A.237, G.303, L.304, F.306, A.348, E.350, S.351, S.377, G.378, K.382 Ligands: X9D.4 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:E.109, B:E.109, B:T.110, B:G.111, 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:S.235, B:S.235, B:N.236, B:N.236, B:S.377 Water bridges: B:A.237, B:A.237 Salt bridges: B:H.86, B:K.87 pi-Stacking: B:H.86, B:F.306 X9D.23: 32 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, G.116, L.166, C.170, 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.351, S.377, G.378, K.382 Ligands: VE4.24 28 PLIP interactions: 28 interactions with chain D Hydrophobic interactions: D:A.85, D:L.166, D:T.190, D:F.306, D:E.350 Hydrogen bonds: 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:S.235, D:S.235, D:N.236, D:N.236, D:S.377 Water bridges: D:A.237 Salt bridges: D:H.86, D:K.87 pi-Stacking: D:H.86, D:F.306 X9D.24: 33 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, C.170, G.189, T.190, A.191, C.230, V.231, G.232, G.233, G.234, S.235, N.236, A.237, G.303, L.304, F.306, A.348, E.350, S.351, S.377, G.378, K.382 Ligands: X9D.23 28 PLIP interactions: 28 interactions with chain D Hydrophobic interactions: D:A.85, D:L.166, D:T.190, D:F.306, D:E.350 Hydrogen bonds: D:K.87, D:E.109, D:T.110, D:G.111, 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:S.235, D:S.235, D:N.236, D:N.236, D:S.377 Water bridges: D:A.237, D:A.237 Salt bridges: D:H.86, D:K.87 pi-Stacking: D:H.86, D:F.306

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

NA.6: 6 residues within 4Å: Chain B: G.232, G.268, P.270, F.306, S.308, V.309 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.232, B:S.308 NA.25: 6 residues within 4Å: Chain D: G.232, G.268, P.270, F.306, S.308, V.309 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.308, D:S.308

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Phillips, R.S. et al., Structural Basis of the Stereochemistry of Inhibition of Tryptophan Synthase by Tryptophan and Derivatives. Biochemistry (2021)

Release Date

2021-02-03

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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