SMTL ID : 6xin.1

The crystal structure of tryptophan synthase from Salmonella enterica serovar typhimurium in complex with (2S)-3-Amino-3-imino-2-phenyldiazenylpropanamide at the enzyme alpha-site.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

hetero-2-2-mer

Ligands

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

CL.1: 4 residues within 4Å: Chain A: H.92, P.93, T.94, I.95 Ligand excluded by PLIP CL.2: 5 residues within 4Å: Chain A: A.167, G.170, H.204, A.206 Ligands: EDO.21 Ligand excluded by PLIP CL.3: 1 residues within 4Å: Chain A: I.153 Ligand excluded by PLIP CL.4: 2 residues within 4Å: Chain A: F.72, V.76 Ligand excluded by PLIP CL.5: 1 residues within 4Å: Chain A: S.168 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain A: E.49, L.100, Y.175, G.234 Ligand excluded by PLIP CL.27: 2 residues within 4Å: Chain B: V.325, S.326 Ligand excluded by PLIP CL.28: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.29: 2 residues within 4Å: Chain B: D.38, R.100 Ligand excluded by PLIP CL.30: 3 residues within 4Å: Chain B: E.172, R.175, D.176 Ligand excluded by PLIP CL.31: 1 residues within 4Å: Ligands: EDO.56 Ligand excluded by PLIP CL.32: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.33: 2 residues within 4Å: Chain B: G.127, L.128 Ligand excluded by PLIP CL.34: 5 residues within 4Å: Chain B: G.10, E.11, F.12, Y.315, S.318 Ligand excluded by PLIP CL.61: 4 residues within 4Å: Chain C: H.92, P.93, T.94, I.95 Ligand excluded by PLIP CL.62: 5 residues within 4Å: Chain C: A.167, G.170, H.204, A.206 Ligands: EDO.81 Ligand excluded by PLIP CL.63: 1 residues within 4Å: Chain C: I.153 Ligand excluded by PLIP CL.64: 2 residues within 4Å: Chain C: F.72, V.76 Ligand excluded by PLIP CL.65: 1 residues within 4Å: Chain C: S.168 Ligand excluded by PLIP CL.66: 4 residues within 4Å: Chain C: E.49, L.100, Y.175, G.234 Ligand excluded by PLIP CL.87: 2 residues within 4Å: Chain D: V.325, S.326 Ligand excluded by PLIP CL.88: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.89: 2 residues within 4Å: Chain D: D.38, R.100 Ligand excluded by PLIP CL.90: 3 residues within 4Å: Chain D: E.172, R.175, D.176 Ligand excluded by PLIP CL.91: 1 residues within 4Å: Ligands: EDO.116 Ligand excluded by PLIP CL.92: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.93: 2 residues within 4Å: Chain D: G.127, L.128 Ligand excluded by PLIP CL.94: 5 residues within 4Å: Chain D: G.10, E.11, F.12, Y.315, S.318 Ligand excluded by PLIP

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

DMS.7: 5 residues within 4Å: Chain A: P.78, A.79, F.82, F.114, R.117 Ligand excluded by PLIP DMS.8: 5 residues within 4Å: Chain A: L.58, A.59 Chain B: P.18, S.178 Ligands: V41.58 Ligand excluded by PLIP DMS.9: 8 residues within 4Å: Chain A: F.22, T.24, G.51, V.52, D.60, I.64, N.68, L.100 Ligand excluded by PLIP DMS.10: 7 residues within 4Å: Chain A: F.107, I.111, P.138, F.139 Chain B: Y.16, I.278, K.283 Ligand excluded by PLIP DMS.11: 5 residues within 4Å: Chain A: N.12, R.15, E.16, G.17, V.224 Ligand excluded by PLIP DMS.12: 4 residues within 4Å: Chain A: R.164, A.167, S.168, Y.203 Ligand excluded by PLIP DMS.13: 5 residues within 4Å: Chain A: I.30, A.74, G.75, V.76, Q.80 Ligand excluded by PLIP DMS.14: 4 residues within 4Å: Chain A: L.34, K.35, D.38, K.91 Ligand excluded by PLIP DMS.15: 6 residues within 4Å: Chain A: I.30, L.34, Q.80, E.83, M.84, L.87 Ligand excluded by PLIP DMS.16: 4 residues within 4Å: Chain A: N.108, N.109 Chain B: R.275, A.290 Ligand excluded by PLIP DMS.35: 4 residues within 4Å: Chain B: H.357, K.360, E.364 Ligands: EDO.57 Ligand excluded by PLIP DMS.36: 5 residues within 4Å: Chain B: Q.42, F.45, A.46, L.49, M.207 Ligand excluded by PLIP DMS.37: 9 residues within 4Å: Chain B: K.50, G.54, R.55, P.56 Chain D: P.56, T.57, A.58, Q.215 Ligands: DMS.97 Ligand excluded by PLIP DMS.38: 4 residues within 4Å: Chain B: P.56, E.211, A.214, Q.215 Ligand excluded by PLIP DMS.39: 5 residues within 4Å: Chain B: I.262, G.265, H.267, H.273 Ligands: EDO.52 Ligand excluded by PLIP DMS.40: 5 residues within 4Å: Chain B: Q.36, K.37, D.38, P.39, Q.42 Ligand excluded by PLIP DMS.41: 1 residues within 4Å: Chain B: H.273 Ligand excluded by PLIP DMS.42: 3 residues within 4Å: Chain B: Y.8, G.10, E.11 Ligand excluded by PLIP DMS.43: 7 residues within 4Å: Chain B: L.5, N.6, Y.8, F.9, H.195, T.199, R.202 Ligand excluded by PLIP DMS.44: 4 residues within 4Å: Chain B: T.3, L.4, L.5, N.6 Ligand excluded by PLIP DMS.45: 7 residues within 4Å: Chain B: T.60, K.61 Chain D: D.47, L.48, N.51, Y.52, L.125 Ligand excluded by PLIP DMS.46: 4 residues within 4Å: Chain B: F.32, Q.36, R.202, E.203 Ligand excluded by PLIP DMS.47: 4 residues within 4Å: Chain B: F.41, Q.44, L.96, R.100 Ligand excluded by PLIP DMS.48: 5 residues within 4Å: Chain B: I.65, T.338, H.342, M.362, R.363 Ligand excluded by PLIP DMS.67: 5 residues within 4Å: Chain C: P.78, A.79, F.82, F.114, R.117 Ligand excluded by PLIP DMS.68: 5 residues within 4Å: Chain C: L.58, A.59 Chain D: P.18, S.178 Ligands: V41.118 Ligand excluded by PLIP DMS.69: 8 residues within 4Å: Chain C: F.22, T.24, G.51, V.52, D.60, I.64, N.68, L.100 Ligand excluded by PLIP DMS.70: 7 residues within 4Å: Chain C: F.107, I.111, P.138, F.139 Chain D: Y.16, I.278, K.283 Ligand excluded by PLIP DMS.71: 5 residues within 4Å: Chain C: N.12, R.15, E.16, G.17, V.224 Ligand excluded by PLIP DMS.72: 4 residues within 4Å: Chain C: R.164, A.167, S.168, Y.203 Ligand excluded by PLIP DMS.73: 5 residues within 4Å: Chain C: I.30, A.74, G.75, V.76, Q.80 Ligand excluded by PLIP DMS.74: 4 residues within 4Å: Chain C: L.34, K.35, D.38, K.91 Ligand excluded by PLIP DMS.75: 6 residues within 4Å: Chain C: I.30, L.34, Q.80, E.83, M.84, L.87 Ligand excluded by PLIP DMS.76: 4 residues within 4Å: Chain C: N.108, N.109 Chain D: R.275, A.290 Ligand excluded by PLIP DMS.95: 4 residues within 4Å: Chain D: H.357, K.360, E.364 Ligands: EDO.117 Ligand excluded by PLIP DMS.96: 5 residues within 4Å: Chain D: Q.42, F.45, A.46, L.49, M.207 Ligand excluded by PLIP DMS.97: 9 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.37 Ligand excluded by PLIP DMS.98: 4 residues within 4Å: Chain D: P.56, E.211, A.214, Q.215 Ligand excluded by PLIP DMS.99: 5 residues within 4Å: Chain D: I.262, G.265, H.267, H.273 Ligands: EDO.112 Ligand excluded by PLIP DMS.100: 5 residues within 4Å: Chain D: Q.36, K.37, D.38, P.39, Q.42 Ligand excluded by PLIP DMS.101: 1 residues within 4Å: Chain D: H.273 Ligand excluded by PLIP DMS.102: 3 residues within 4Å: Chain D: Y.8, G.10, E.11 Ligand excluded by PLIP DMS.103: 7 residues within 4Å: Chain D: L.5, N.6, Y.8, F.9, H.195, T.199, R.202 Ligand excluded by PLIP DMS.104: 4 residues within 4Å: Chain D: T.3, L.4, L.5, N.6 Ligand excluded by PLIP DMS.105: 7 residues within 4Å: Chain B: D.47, L.48, N.51, Y.52, L.125 Chain D: T.60, K.61 Ligand excluded by PLIP DMS.106: 4 residues within 4Å: Chain D: F.32, Q.36, R.202, E.203 Ligand excluded by PLIP DMS.107: 4 residues within 4Å: Chain D: F.41, Q.44, L.96, R.100 Ligand excluded by PLIP DMS.108: 5 residues within 4Å: Chain D: I.65, T.338, H.342, M.362, R.363 Ligand excluded by PLIP

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

EDO.17: 5 residues within 4Å: Chain A: F.107, N.108, G.110 Chain B: R.275, V.276 Ligand excluded by PLIP EDO.18: 8 residues within 4Å: Chain A: M.1, E.2, R.3, E.119, G.122, V.123, D.124, N.147 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain A: R.3, N.6, P.93, T.94 Ligand excluded by PLIP EDO.20: 3 residues within 4Å: Chain A: H.204, A.205 Ligands: EDO.21 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain A: R.171, G.172, A.206 Ligands: CL.2, EDO.20 Ligand excluded by PLIP EDO.22: 4 residues within 4Å: Chain A: R.3, R.89, E.90, P.93 Ligand excluded by PLIP EDO.23: 1 residues within 4Å: Chain A: P.28 Ligand excluded by PLIP EDO.49: 4 residues within 4Å: Chain B: Q.27, E.30, A.31, M.101 Ligand excluded by PLIP EDO.50: 5 residues within 4Å: Chain B: I.245, N.246, T.248, I.319, R.321 Ligand excluded by PLIP EDO.51: 6 residues within 4Å: Chain B: H.273, G.274, M.286, M.287, Q.288 Ligands: EDO.52 Ligand excluded by PLIP EDO.52: 5 residues within 4Å: Chain B: K.272, H.273, G.274 Ligands: DMS.39, EDO.51 Ligand excluded by PLIP EDO.53: 2 residues within 4Å: Chain B: Q.36, Q.42 Ligand excluded by PLIP EDO.54: 3 residues within 4Å: Chain B: T.248, G.320, R.321 Ligand excluded by PLIP EDO.55: 7 residues within 4Å: Chain A: E.134, P.155, N.157, L.162 Chain B: Q.19, M.22, P.23 Ligand excluded by PLIP EDO.56: 8 residues within 4Å: Chain B: K.87, T.110, G.111, A.112, G.113, Q.114, H.115 Ligands: CL.31 Ligand excluded by PLIP EDO.57: 6 residues within 4Å: Chain B: I.253, D.323, V.325, H.357, M.361 Ligands: DMS.35 Ligand excluded by PLIP EDO.77: 5 residues within 4Å: Chain C: F.107, N.108, G.110 Chain D: R.275, V.276 Ligand excluded by PLIP EDO.78: 8 residues within 4Å: Chain C: M.1, E.2, R.3, E.119, G.122, V.123, D.124, N.147 Ligand excluded by PLIP EDO.79: 4 residues within 4Å: Chain C: R.3, N.6, P.93, T.94 Ligand excluded by PLIP EDO.80: 3 residues within 4Å: Chain C: H.204, A.205 Ligands: EDO.81 Ligand excluded by PLIP EDO.81: 5 residues within 4Å: Chain C: R.171, G.172, A.206 Ligands: CL.62, EDO.80 Ligand excluded by PLIP EDO.82: 4 residues within 4Å: Chain C: R.3, R.89, E.90, P.93 Ligand excluded by PLIP EDO.83: 1 residues within 4Å: Chain C: P.28 Ligand excluded by PLIP EDO.109: 4 residues within 4Å: Chain D: Q.27, E.30, A.31, M.101 Ligand excluded by PLIP EDO.110: 5 residues within 4Å: Chain D: I.245, N.246, T.248, I.319, R.321 Ligand excluded by PLIP EDO.111: 6 residues within 4Å: Chain D: H.273, G.274, M.286, M.287, Q.288 Ligands: EDO.112 Ligand excluded by PLIP EDO.112: 5 residues within 4Å: Chain D: K.272, H.273, G.274 Ligands: DMS.99, EDO.111 Ligand excluded by PLIP EDO.113: 2 residues within 4Å: Chain D: Q.36, Q.42 Ligand excluded by PLIP EDO.114: 3 residues within 4Å: Chain D: T.248, G.320, R.321 Ligand excluded by PLIP EDO.115: 7 residues within 4Å: Chain C: E.134, P.155, N.157, L.162 Chain D: Q.19, M.22, P.23 Ligand excluded by PLIP EDO.116: 8 residues within 4Å: Chain D: K.87, T.110, G.111, A.112, G.113, Q.114, H.115 Ligands: CL.91 Ligand excluded by PLIP EDO.117: 6 residues within 4Å: Chain D: I.253, D.323, V.325, H.357, M.361 Ligands: DMS.95 Ligand excluded by PLIP

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

PGE.24: 5 residues within 4Å: Chain A: S.221, R.225, A.264, A.265, R.267 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.221, A:R.225, A:R.225 PGE.84: 5 residues within 4Å: Chain C: S.221, R.225, A.264, A.265, R.267 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.221, C:R.225, C:R.225

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

PEG.25: 3 residues within 4Å: Chain A: P.217, S.257, F.258 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.257 PEG.85: 3 residues within 4Å: Chain C: P.217, S.257, F.258 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.257

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

PLP.26: 17 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, A.348, E.350, S.377, G.378 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:A.85, B:K.87, B:A.348 Hydrogen bonds: 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:K.87, B:Q.114, B:G.233, B:G.233, B:S.235, B:S.235, B:A.237 Salt bridges: B:H.86 pi-Stacking: B:H.86 PLP.86: 17 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, A.348, E.350, S.377, G.378 21 PLIP interactions: 21 interactions with chain D Hydrophobic interactions: D:A.85, D:K.87, D:A.348 Hydrogen bonds: D:K.87, D:G.232, D:G.233, D:G.233, D:G.234, D:S.235, D:S.235, D:N.236, D:N.236, D:S.377 Water bridges: D:Q.114, D:T.190, D:T.190, D:S.235, D:S.235, D:A.237 Salt bridges: D:H.86 pi-Stacking: D:H.86

2 x V41: (2R,3Z)-3-amino-3-imino-2-[(E)-phenyldiazenyl]propanamide(Non-covalent)

V41.58: 15 residues within 4Å: Chain A: L.58, A.59, D.130 Chain B: Y.16, V.17, P.18, L.21, L.174, W.177, Y.186, L.188, P.194, F.280, G.281 Ligands: DMS.8 13 PLIP interactions: 11 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:V.17, B:L.21, B:L.174, B:L.174, B:W.177, B:Y.186, B:Y.186, B:L.188, B:P.194, B:F.280 Hydrogen bonds: B:G.281, A:L.58 Water bridges: A:D.130 V41.118: 15 residues within 4Å: Chain C: L.58, A.59, D.130 Chain D: Y.16, V.17, P.18, L.21, L.174, W.177, Y.186, L.188, P.194, F.280, G.281 Ligands: DMS.68 15 PLIP interactions: 11 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:V.17, D:L.21, D:L.174, D:L.174, D:W.177, D:Y.186, D:Y.186, D:L.188, D:P.194, D:F.280 Hydrogen bonds: D:G.281, C:L.58 Water bridges: C:D.130, C:D.130, C:D.130

4 x CS: CESIUM ION(Non-covalent)

CS.59: 7 residues within 4Å: Chain B: V.231, G.232, G.268, P.270, 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.60: 3 residues within 4Å: Chain B: T.66, T.69, T.71 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.71, H2O.19, H2O.20 CS.119: 7 residues within 4Å: Chain D: V.231, G.232, G.268, P.270, 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.120: 3 residues within 4Å: Chain D: T.66, T.69, T.71 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:T.71, H2O.43, H2O.44

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hilario, E. et al., The crystal structure of tryptophan synthase from Salmonella enterica serovar typhimurium in complex with (2S)-3-Amino-3-imino-2-phenyldiazenylpropanamide at the enzyme alpha-site. To Be Published

Release Date

2021-06-23

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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