SMTL ID : 7jll.1

The internal aldimine crystal structure of Salmonella typhimurium Tryptophan Synthase mutant beta-S377A in complex with inhibitor 2-({[4-(trifluoromethoxy)phenyl]sulfonyl}amino)ethyl dihydrogen phosphate (F9F) at the alpha-site, Cesium ion at the metal coordination site and L-Tryptophan at the enzyme beta-site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

hetero-2-2-mer

Ligands

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

DMS.1: 5 residues within 4Å: Chain A: I.41, H.92, P.93, T.94, I.95 Ligand excluded by PLIP DMS.2: 7 residues within 4Å: Chain A: V.128, S.136, F.139, R.140, P.150, I.151, F.152 Ligand excluded by PLIP DMS.3: 4 residues within 4Å: Chain A: S.55, L.69, F.72 Chain B: G.162 Ligand excluded by PLIP DMS.4: 6 residues within 4Å: Chain A: L.191, P.192, L.193, H.194, A.222, A.226 Ligand excluded by PLIP DMS.5: 4 residues within 4Å: Chain A: L.34, K.35, D.38, K.91 Ligand excluded by PLIP DMS.6: 4 residues within 4Å: Chain A: R.15, E.16, V.224, A.268 Ligand excluded by PLIP DMS.10: 8 residues within 4Å: Chain A: E.2, R.3, E.119, G.122, V.123, D.124, H.146, N.147 Ligand excluded by PLIP DMS.11: 6 residues within 4Å: Chain A: E.2, E.5, N.147, I.148, A.149, R.171 Ligand excluded by PLIP DMS.12: 2 residues within 4Å: Chain A: H.204, A.205 Ligand excluded by PLIP DMS.13: 2 residues within 4Å: Chain A: H.194, R.225 Ligand excluded by PLIP DMS.25: 4 residues within 4Å: Chain B: Y.133, E.172, R.175, D.176 Ligand excluded by PLIP DMS.26: 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.84 Ligand excluded by PLIP DMS.27: 5 residues within 4Å: Chain B: Q.42, F.45, A.46, L.49, M.207 Ligand excluded by PLIP DMS.28: 2 residues within 4Å: Chain B: K.99, R.100 Ligand excluded by PLIP DMS.29: 4 residues within 4Å: Chain B: I.262, G.265, H.267, H.273 Ligand excluded by PLIP DMS.30: 4 residues within 4Å: Chain B: T.3, L.4, L.5, N.6 Ligand excluded by PLIP DMS.31: 6 residues within 4Å: Chain B: Q.36, K.37, D.38, P.39, Q.42 Ligands: CL.54 Ligand excluded by PLIP DMS.32: 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.35: 3 residues within 4Å: Chain B: P.56, E.211, Q.215 Ligand excluded by PLIP DMS.36: 5 residues within 4Å: Chain B: P.23, A.24, Q.27, Y.181, E.182 Ligand excluded by PLIP DMS.37: 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.38: 7 residues within 4Å: Chain A: S.180 Chain B: S.178, G.179, S.180, Y.181, E.182 Ligands: TRP.9 Ligand excluded by PLIP DMS.39: 3 residues within 4Å: Chain B: A.290, D.291 Ligands: CL.52 Ligand excluded by PLIP DMS.40: 5 residues within 4Å: Chain B: T.248, S.249, V.250, G.251, R.321 Ligand excluded by PLIP DMS.59: 5 residues within 4Å: Chain C: I.41, H.92, P.93, T.94, I.95 Ligand excluded by PLIP DMS.60: 7 residues within 4Å: Chain C: V.128, S.136, F.139, R.140, P.150, I.151, F.152 Ligand excluded by PLIP DMS.61: 4 residues within 4Å: Chain C: S.55, L.69, F.72 Chain D: G.162 Ligand excluded by PLIP DMS.62: 6 residues within 4Å: Chain C: L.191, P.192, L.193, H.194, A.222, A.226 Ligand excluded by PLIP DMS.63: 4 residues within 4Å: Chain C: L.34, K.35, D.38, K.91 Ligand excluded by PLIP DMS.64: 4 residues within 4Å: Chain C: R.15, E.16, V.224, A.268 Ligand excluded by PLIP DMS.68: 8 residues within 4Å: Chain C: E.2, R.3, E.119, G.122, V.123, D.124, H.146, N.147 Ligand excluded by PLIP DMS.69: 6 residues within 4Å: Chain C: E.2, E.5, N.147, I.148, A.149, R.171 Ligand excluded by PLIP DMS.70: 2 residues within 4Å: Chain C: H.204, A.205 Ligand excluded by PLIP DMS.71: 2 residues within 4Å: Chain C: H.194, R.225 Ligand excluded by PLIP DMS.83: 4 residues within 4Å: Chain D: Y.133, E.172, R.175, D.176 Ligand excluded by PLIP DMS.84: 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.26 Ligand excluded by PLIP DMS.85: 5 residues within 4Å: Chain D: Q.42, F.45, A.46, L.49, M.207 Ligand excluded by PLIP DMS.86: 2 residues within 4Å: Chain D: K.99, R.100 Ligand excluded by PLIP DMS.87: 4 residues within 4Å: Chain D: I.262, G.265, H.267, H.273 Ligand excluded by PLIP DMS.88: 4 residues within 4Å: Chain D: T.3, L.4, L.5, N.6 Ligand excluded by PLIP DMS.89: 6 residues within 4Å: Chain D: Q.36, K.37, D.38, P.39, Q.42 Ligands: CL.112 Ligand excluded by PLIP DMS.90: 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.93: 3 residues within 4Å: Chain D: P.56, E.211, Q.215 Ligand excluded by PLIP DMS.94: 5 residues within 4Å: Chain D: P.23, A.24, Q.27, Y.181, E.182 Ligand excluded by PLIP DMS.95: 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.96: 7 residues within 4Å: Chain C: S.180 Chain D: S.178, G.179, S.180, Y.181, E.182 Ligands: TRP.67 Ligand excluded by PLIP DMS.97: 3 residues within 4Å: Chain D: A.290, D.291 Ligands: CL.110 Ligand excluded by PLIP DMS.98: 5 residues within 4Å: Chain D: T.248, S.249, V.250, G.251, R.321 Ligand excluded by PLIP

2 x F9F: 2-({[4-(TRIFLUOROMETHOXY)PHENYL]SULFONYL}AMINO)ETHYL DIHYDROGEN PHOSPHATE(Non-covalent)

F9F.7: 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 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.127, 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.65: 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 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:L.127, 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

6 x CS: CESIUM ION(Non-covalent)

CS.8: 4 residues within 4Å: Chain A: A.167, G.170, H.204, A.206 No protein-ligand interaction detected (PLIP) CS.44: 3 residues within 4Å: Chain B: T.66, T.69, T.71 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:T.66, B:T.66, B:T.69, B:T.71, H2O.24 CS.45: 7 residues within 4Å: Chain B: V.231, G.232, G.268, P.270, L.304, F.306, S.308 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:G.232, B:F.306 CS.66: 4 residues within 4Å: Chain C: A.167, G.170, H.204, A.206 No protein-ligand interaction detected (PLIP) CS.102: 3 residues within 4Å: Chain D: T.66, T.69, T.71 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:T.66, D:T.66, D:T.69, D:T.71, H2O.52 CS.103: 7 residues within 4Å: Chain D: V.231, G.232, G.268, P.270, L.304, F.306, S.308 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:G.232, D:F.306

4 x TRP: TRYPTOPHAN(Non-covalent)

TRP.9: 9 residues within 4Å: Chain A: P.156, N.157, R.179, S.180, L.191 Chain B: I.20, Y.181, E.182 Ligands: DMS.38 9 PLIP interactions: 5 interactions with chain A, 2 Ligand-Ligand interactions, 2 interactions with chain B Hydrophobic interactions: A:P.156, A:P.156, A:N.157, A:L.191, B:I.20 Hydrogen bonds: A:S.180, W.9, W.9, B:E.182 TRP.33: 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.34 14 PLIP interactions: 14 interactions with chain B, Hydrophobic interactions: B:L.166, B:T.190, B:F.306 Hydrogen bonds: B:E.109, B:T.110, B:G.111, B:A.112, B:G.113, B:Q.114, B:H.115, B:A.302 Water bridges: B:K.87 Salt bridges: B:K.87 pi-Stacking: B:F.306 TRP.67: 9 residues within 4Å: Chain C: P.156, N.157, R.179, S.180, L.191 Chain D: I.20, Y.181, E.182 Ligands: DMS.96 9 PLIP interactions: 5 interactions with chain C, 2 Ligand-Ligand interactions, 2 interactions with chain D Hydrophobic interactions: C:P.156, C:P.156, C:N.157, C:L.191, D:I.20 Hydrogen bonds: C:S.180, W.67, W.67, D:E.182 TRP.91: 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.92 14 PLIP interactions: 14 interactions with chain D, Hydrophobic interactions: D:L.166, D:T.190, D:F.306 Hydrogen bonds: D:E.109, D:E.109, D:G.111, D:A.112, D:G.113, D:Q.114, D:H.115, D:A.302 Water bridges: D:K.87 Salt bridges: D:K.87 pi-Stacking: D:F.306

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

PEG.14: 5 residues within 4Å: Chain A: P.217, E.254, S.257, F.258, A.261 No protein-ligand interaction detected (PLIP) PEG.72: 5 residues within 4Å: Chain C: P.217, E.254, S.257, F.258, A.261 No protein-ligand interaction detected (PLIP)

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

CL.15: 1 residues within 4Å: Chain A: S.180 Ligand excluded by PLIP CL.16: 1 residues within 4Å: Chain A: R.256 Ligand excluded by PLIP CL.17: 1 residues within 4Å: Chain A: I.30 Ligand excluded by PLIP CL.18: 1 residues within 4Å: Chain A: S.168 Ligand excluded by PLIP CL.19: 2 residues within 4Å: Chain A: N.66 Chain B: H.160 Ligand excluded by PLIP CL.20: 1 residues within 4Å: Chain A: A.268 Ligand excluded by PLIP CL.21: 3 residues within 4Å: Chain A: R.179, G.181, V.182 Ligand excluded by PLIP CL.22: 3 residues within 4Å: Chain A: V.133, R.140, Y.169 Ligand excluded by PLIP CL.23: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.24: 2 residues within 4Å: Chain A: P.192, L.196 Ligand excluded by PLIP CL.46: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.47: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.48: 1 residues within 4Å: Chain B: R.141 Ligand excluded by PLIP CL.49: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.50: 1 residues within 4Å: Chain B: R.150 Ligand excluded by PLIP CL.51: 3 residues within 4Å: Chain B: K.219, E.220, G.221 Ligand excluded by PLIP CL.52: 3 residues within 4Å: Chain B: A.290, D.291 Ligands: DMS.39 Ligand excluded by PLIP CL.53: 3 residues within 4Å: Chain B: Q.36, Q.42 Ligands: CL.54 Ligand excluded by PLIP CL.54: 2 residues within 4Å: Ligands: DMS.31, CL.53 Ligand excluded by PLIP CL.55: 5 residues within 4Å: Chain B: G.10, E.11, F.12, Y.315, S.318 Ligand excluded by PLIP CL.56: 2 residues within 4Å: Chain B: M.287, Q.288 Ligand excluded by PLIP CL.57: 3 residues within 4Å: Chain B: I.245, I.319, R.321 Ligand excluded by PLIP CL.58: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.73: 1 residues within 4Å: Chain C: S.180 Ligand excluded by PLIP CL.74: 1 residues within 4Å: Chain C: R.256 Ligand excluded by PLIP CL.75: 1 residues within 4Å: Chain C: I.30 Ligand excluded by PLIP CL.76: 1 residues within 4Å: Chain C: S.168 Ligand excluded by PLIP CL.77: 2 residues within 4Å: Chain C: N.66 Chain D: H.160 Ligand excluded by PLIP CL.78: 1 residues within 4Å: Chain C: A.268 Ligand excluded by PLIP CL.79: 3 residues within 4Å: Chain C: R.179, G.181, V.182 Ligand excluded by PLIP CL.80: 3 residues within 4Å: Chain C: V.133, R.140, Y.169 Ligand excluded by PLIP CL.81: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.82: 2 residues within 4Å: Chain C: P.192, L.196 Ligand excluded by PLIP CL.104: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.105: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.106: 1 residues within 4Å: Chain D: R.141 Ligand excluded by PLIP CL.107: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.108: 1 residues within 4Å: Chain D: R.150 Ligand excluded by PLIP CL.109: 3 residues within 4Å: Chain D: K.219, E.220, G.221 Ligand excluded by PLIP CL.110: 3 residues within 4Å: Chain D: A.290, D.291 Ligands: DMS.97 Ligand excluded by PLIP CL.111: 3 residues within 4Å: Chain D: Q.36, Q.42 Ligands: CL.112 Ligand excluded by PLIP CL.112: 2 residues within 4Å: Ligands: DMS.89, CL.111 Ligand excluded by PLIP CL.113: 5 residues within 4Å: Chain D: G.10, E.11, F.12, Y.315, S.318 Ligand excluded by PLIP CL.114: 2 residues within 4Å: Chain D: M.287, Q.288 Ligand excluded by PLIP CL.115: 3 residues within 4Å: Chain D: I.245, I.319, R.321 Ligand excluded by PLIP CL.116: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

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

PLP.34: 19 residues within 4Å: Chain B: A.85, H.86, K.87, 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.351, A.377, G.378 Ligands: TRP.33 18 PLIP interactions: 2 Ligand-Ligand interactions, 16 interactions with chain B Hydrophobic interactions: W.33, B:K.87, B:A.348, B:A.377 Water bridges: W.33, B:S.235, B:S.235, B:A.237 Hydrogen bonds: B:G.232, B:G.233, B:G.233, B:G.234, B:S.235, B:N.236, B:N.236 Salt bridges: B:H.86, B:K.87 pi-Stacking: B:H.86 PLP.92: 19 residues within 4Å: Chain D: A.85, H.86, K.87, 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.351, A.377, G.378 Ligands: TRP.91 19 PLIP interactions: 17 interactions with chain D, 2 Ligand-Ligand interactions Hydrophobic interactions: D:K.87, D:A.348, D:A.377, W.91 Hydrogen bonds: D:T.190, D:G.232, D:G.233, D:G.233, D:G.234, D:S.235, D:N.236, D:N.236 Water bridges: D:S.235, D:S.235, D:A.237, W.91 Salt bridges: D:H.86, D:K.87 pi-Stacking: D:H.86

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

EDO.41: 5 residues within 4Å: Chain B: G.259, H.260, T.328, D.329, D.330 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.259, B:T.328, B:D.330 EDO.42: 5 residues within 4Å: Chain B: N.51, Y.52, L.125 Chain D: T.60, K.61 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:K.61 Water bridges: D:K.61, D:Q.63, B:D.47, B:N.51 EDO.43: 4 residues within 4Å: Chain B: S.143, V.146, F.147, R.150 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.150 Water bridges: B:S.143 EDO.99: 5 residues within 4Å: Chain D: G.259, H.260, T.328, D.329, D.330 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:G.259, D:D.330, D:D.330 Water bridges: D:D.329 EDO.100: 5 residues within 4Å: Chain B: T.60, K.61 Chain D: N.51, Y.52, L.125 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain B Water bridges: D:D.47, D:N.51, B:K.61, B:Q.63 Hydrogen bonds: B:K.61 EDO.101: 4 residues within 4Å: Chain D: S.143, V.146, F.147, R.150 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.150 Water bridges: D:S.143

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hilario, E. et al., The internal aldimine crystal structure of Salmonella typhimurium Tryptophan Synthase mutant beta-S377A in complex with inhibitor 2-({[4-(trifluoromethoxy)phenyl]sulfonyl}amino)ethyl dihydrogen phosphate (F9F) at the alpha-site, Cesium ion at the metal coordination site and L-Tryptophan at the enzyme beta-site. To be Published

Release Date

2021-08-04

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

Related Entries With Identical Sequence