SMTL ID : 6xnc.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.11 Å

Oligo State

hetero-2-2-mer

Ligands

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

DMS.1: 7 residues within 4Å: Chain A: R.3, E.119, G.122, V.123, D.124, H.146, N.147 Ligand excluded by PLIP DMS.2: 3 residues within 4Å: Chain A: L.144, A.149, R.171 Ligand excluded by PLIP DMS.3: 4 residues within 4Å: Chain A: N.12, R.15, E.16, V.224 Ligand excluded by PLIP DMS.4: 5 residues within 4Å: Chain A: R.179, S.180, N.187 Chain B: G.179 Ligands: DMS.13 Ligand excluded by PLIP DMS.5: 9 residues within 4Å: Chain A: V.126, V.128, V.131, S.136, F.139, R.140, P.150, I.151, F.152 Ligand excluded by PLIP DMS.6: 4 residues within 4Å: Chain A: N.66, R.70, E.242, L.245 Ligand excluded by PLIP DMS.7: 6 residues within 4Å: Chain A: L.100, L.127, A.129, I.153, Y.175, F.212 Ligand excluded by PLIP DMS.10: 4 residues within 4Å: Chain B: Q.42, F.45, A.46, L.49 Ligand excluded by PLIP DMS.11: 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.12: 3 residues within 4Å: Chain B: P.56, A.214, Q.215 Ligand excluded by PLIP DMS.13: 6 residues within 4Å: Chain A: S.180 Chain B: G.179, S.180, Y.181, E.182 Ligands: DMS.4 Ligand excluded by PLIP DMS.14: 4 residues within 4Å: Chain B: L.391, I.397 Chain D: F.147, R.150 Ligand excluded by PLIP DMS.15: 2 residues within 4Å: Chain B: Q.27, Y.181 Ligand excluded by PLIP DMS.16: 5 residues within 4Å: Chain B: R.141, Q.142, P.144, F.385, T.386 Ligand excluded by PLIP DMS.17: 1 residues within 4Å: Chain B: E.182 Ligand excluded by PLIP DMS.18: 5 residues within 4Å: Chain B: P.270, L.271, G.274, P.285 Ligands: DMS.28 Ligand excluded by PLIP DMS.19: 5 residues within 4Å: Chain B: Q.44, D.47 Chain D: Q.63 Ligands: DMS.22, DMS.30 Ligand excluded by PLIP DMS.20: 3 residues within 4Å: Chain B: H.260, E.266, Y.298 Ligand excluded by PLIP DMS.21: 2 residues within 4Å: Chain B: E.11, F.12 Ligand excluded by PLIP DMS.22: 5 residues within 4Å: Chain B: D.47, N.51 Chain D: T.60, K.61 Ligands: DMS.19 Ligand excluded by PLIP DMS.23: 2 residues within 4Å: Chain B: G.10, E.11 Ligand excluded by PLIP DMS.24: 3 residues within 4Å: Chain B: Q.36, K.37, P.39 Ligand excluded by PLIP DMS.25: 7 residues within 4Å: Chain B: K.50, G.54, R.55, P.56 Chain D: P.56, T.57, Q.215 Ligand excluded by PLIP DMS.26: 5 residues within 4Å: Chain B: P.158, V.159, H.160, S.161, E.172 Ligand excluded by PLIP DMS.27: 4 residues within 4Å: Chain B: F.41, Q.44, L.96, R.100 Ligand excluded by PLIP DMS.28: 4 residues within 4Å: Chain B: K.272, H.273, G.274 Ligands: DMS.18 Ligand excluded by PLIP DMS.29: 1 residues within 4Å: Chain B: H.160 Ligand excluded by PLIP DMS.30: 3 residues within 4Å: Chain B: E.40, D.47 Ligands: DMS.19 Ligand excluded by PLIP DMS.33: 7 residues within 4Å: Chain C: R.3, E.119, G.122, V.123, D.124, H.146, N.147 Ligand excluded by PLIP DMS.34: 3 residues within 4Å: Chain C: L.144, A.149, R.171 Ligand excluded by PLIP DMS.35: 4 residues within 4Å: Chain C: N.12, R.15, E.16, V.224 Ligand excluded by PLIP DMS.36: 5 residues within 4Å: Chain C: R.179, S.180, N.187 Chain D: G.179 Ligands: DMS.45 Ligand excluded by PLIP DMS.37: 9 residues within 4Å: Chain C: V.126, V.128, V.131, S.136, F.139, R.140, P.150, I.151, F.152 Ligand excluded by PLIP DMS.38: 4 residues within 4Å: Chain C: N.66, R.70, E.242, L.245 Ligand excluded by PLIP DMS.39: 6 residues within 4Å: Chain C: L.100, L.127, A.129, I.153, Y.175, F.212 Ligand excluded by PLIP DMS.42: 4 residues within 4Å: Chain D: Q.42, F.45, A.46, L.49 Ligand excluded by PLIP DMS.43: 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.44: 3 residues within 4Å: Chain D: P.56, A.214, Q.215 Ligand excluded by PLIP DMS.45: 6 residues within 4Å: Chain C: S.180 Chain D: G.179, S.180, Y.181, E.182 Ligands: DMS.36 Ligand excluded by PLIP DMS.46: 4 residues within 4Å: Chain B: F.147, R.150 Chain D: L.391, I.397 Ligand excluded by PLIP DMS.47: 2 residues within 4Å: Chain D: Q.27, Y.181 Ligand excluded by PLIP DMS.48: 5 residues within 4Å: Chain D: R.141, Q.142, P.144, F.385, T.386 Ligand excluded by PLIP DMS.49: 1 residues within 4Å: Chain D: E.182 Ligand excluded by PLIP DMS.50: 5 residues within 4Å: Chain D: P.270, L.271, G.274, P.285 Ligands: DMS.60 Ligand excluded by PLIP DMS.51: 5 residues within 4Å: Chain B: Q.63 Chain D: Q.44, D.47 Ligands: DMS.54, DMS.62 Ligand excluded by PLIP DMS.52: 3 residues within 4Å: Chain D: H.260, E.266, Y.298 Ligand excluded by PLIP DMS.53: 2 residues within 4Å: Chain D: E.11, F.12 Ligand excluded by PLIP DMS.54: 5 residues within 4Å: Chain B: T.60, K.61 Chain D: D.47, N.51 Ligands: DMS.51 Ligand excluded by PLIP DMS.55: 2 residues within 4Å: Chain D: G.10, E.11 Ligand excluded by PLIP DMS.56: 3 residues within 4Å: Chain D: Q.36, K.37, P.39 Ligand excluded by PLIP DMS.57: 7 residues within 4Å: Chain B: P.56, T.57, Q.215 Chain D: K.50, G.54, R.55, P.56 Ligand excluded by PLIP DMS.58: 5 residues within 4Å: Chain D: P.158, V.159, H.160, S.161, E.172 Ligand excluded by PLIP DMS.59: 4 residues within 4Å: Chain D: F.41, Q.44, L.96, R.100 Ligand excluded by PLIP DMS.60: 4 residues within 4Å: Chain D: K.272, H.273, G.274 Ligands: DMS.50 Ligand excluded by PLIP DMS.61: 1 residues within 4Å: Chain D: H.160 Ligand excluded by PLIP DMS.62: 3 residues within 4Å: Chain D: E.40, D.47 Ligands: DMS.51 Ligand excluded by PLIP

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

1GP.8: 12 residues within 4Å: Chain A: F.22, I.64, L.100, Y.175, T.183, G.184, F.212, G.213, I.232, S.233, G.234, S.235 8 PLIP interactions: 8 interactions with chain A 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 1GP.40: 12 residues within 4Å: Chain C: F.22, I.64, L.100, Y.175, T.183, G.184, F.212, G.213, I.232, S.233, G.234, S.235 8 PLIP interactions: 8 interactions with chain C 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

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

NA.9: 5 residues within 4Å: Chain B: G.232, G.268, P.270, F.306, S.308 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.306 NA.41: 5 residues within 4Å: Chain D: G.232, G.268, P.270, F.306, S.308 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.308

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)

PLP.31: 19 residues within 4Å: Chain B: A.85, H.86, K.87, Q.114, T.190, C.230, V.231, G.232, G.233, G.234, S.235, N.236, G.303, L.304, A.348, E.350, S.377, G.378 Ligands: TRP.32 20 PLIP interactions: 19 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:K.87, B:A.348, B:E.350, W.32 Hydrogen bonds: B:Q.114, B:T.190, B:G.232, B:G.233, B:G.234, B:S.235, B:S.235, B:N.236, B:N.236, B:S.377 Water bridges: B:S.235, B:S.235, B:A.237 Salt bridges: B:H.86, B:K.87 pi-Stacking: B:H.86 PLP.63: 19 residues within 4Å: Chain D: A.85, H.86, K.87, Q.114, T.190, C.230, V.231, G.232, G.233, G.234, S.235, N.236, G.303, L.304, A.348, E.350, S.377, G.378 Ligands: TRP.64 19 PLIP interactions: 18 interactions with chain D, 1 Ligand-Ligand interactions Hydrophobic interactions: D:K.87, D:A.348, D:E.350, W.64 Hydrogen bonds: D:Q.114, D:G.232, D:G.233, D:G.234, D:S.235, D:S.235, D:N.236, D:N.236, D:S.377 Water bridges: D:S.235, D:S.235, D:A.237 Salt bridges: D:H.86, D:K.87 pi-Stacking: D:H.86

2 x TRP: TRYPTOPHAN(Non-covalent)

TRP.32: 16 residues within 4Å: Chain B: K.87, E.109, T.110, G.111, A.112, G.113, Q.114, H.115, L.166, G.189, T.190, G.233, A.302, G.303, F.306 Ligands: PLP.31 14 PLIP interactions: 12 interactions with chain B, 2 Ligand-Ligand interactions Hydrophobic interactions: B:L.166, B:T.190, B:F.306, B:F.306 Hydrogen bonds: B:E.109, B:G.111, B:A.112, B:G.113, B:Q.114, B:H.115, B:A.302, W.32, W.32 Salt bridges: B:K.87 TRP.64: 16 residues within 4Å: Chain D: K.87, E.109, T.110, G.111, A.112, G.113, Q.114, H.115, L.166, G.189, T.190, G.233, A.302, G.303, F.306 Ligands: PLP.63 14 PLIP interactions: 12 interactions with chain D, 2 Ligand-Ligand interactions Hydrophobic interactions: D:L.166, D:T.190, D:F.306, D:F.306 Hydrogen bonds: D:T.110, D:G.111, D:A.112, D:G.113, D:Q.114, D:H.115, D:A.302, W.64, W.64 Salt bridges: D:K.87

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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