SMTL ID : 7jtt.1

The external aldimine crystal structure of Salmonella typhimurium Tryptophan Synthase mutant beta-S377A in complex F9 inhibitor at the alpha-site and cesium ion at the metal coordination site. The single beta-Q114 rotamer conformation allows a hydrogen bond to form with the PLP oxygen at the position 3 in the ring

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.64 Å

Oligo State

hetero-1-1-mer

Ligands

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

F9F.1: 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.100, A:L.127, 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:I.214, A:I.214, A:A.236 pi-Stacking: A:F.212

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

DMS.2: 8 residues within 4Å: Chain A: V.128, V.131, S.136, F.139, R.140, P.150, I.151, F.152 Ligand excluded by PLIP DMS.3: 5 residues within 4Å: Chain A: S.55, L.69, F.72 Chain B: G.162 Ligands: EDO.35 Ligand excluded by PLIP DMS.4: 5 residues within 4Å: Chain A: I.41, H.92, P.93, T.94, I.95 Ligand excluded by PLIP DMS.5: 9 residues within 4Å: Chain A: M.1, E.2, R.3, E.119, V.123, D.124, H.146, N.147, I.148 Ligand excluded by PLIP DMS.6: 5 residues within 4Å: Chain A: L.34, K.35, D.38, L.87, K.91 Ligand excluded by PLIP DMS.9: 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.10: 4 residues within 4Å: Chain B: K.50, G.54, R.55, P.56 Ligand excluded by PLIP DMS.11: 5 residues within 4Å: Chain B: Q.42, F.45, A.46, L.49, M.207 Ligand excluded by PLIP DMS.12: 6 residues within 4Å: Chain B: I.262, G.265, H.267, H.273 Ligands: DMS.13, EDO.31 Ligand excluded by PLIP DMS.13: 8 residues within 4Å: Chain B: H.267, H.273, G.274, R.275, M.286, M.287, Q.288 Ligands: DMS.12 Ligand excluded by PLIP DMS.14: 9 residues within 4Å: Chain B: A.112, Q.114, Q.142, N.145, A.302, E.350, K.382, D.383 Ligands: DMS.21 Ligand excluded by PLIP DMS.15: 6 residues within 4Å: Chain B: E.109, L.166, G.189, T.190, F.306 Ligands: KOU.27 Ligand excluded by PLIP DMS.16: 2 residues within 4Å: Chain B: T.60, K.61 Ligand excluded by PLIP DMS.17: 1 residues within 4Å: Chain B: G.10 Ligand excluded by PLIP DMS.18: 8 residues within 4Å: Chain B: P.270, L.271, K.272, H.273, G.274, V.276, P.285 Ligands: EDO.31 Ligand excluded by PLIP DMS.19: 5 residues within 4Å: Chain B: S.143, V.146, F.147, R.150 Ligands: DMS.24 Ligand excluded by PLIP DMS.20: 4 residues within 4Å: Chain B: Y.133, E.172, R.175, D.176 Ligand excluded by PLIP DMS.21: 5 residues within 4Å: Chain B: R.141, Q.142, P.144, F.385 Ligands: DMS.14 Ligand excluded by PLIP DMS.22: 5 residues within 4Å: Chain B: Q.36, K.37, D.38, P.39, Q.42 Ligand excluded by PLIP DMS.23: 4 residues within 4Å: Chain B: F.41, Q.44, L.96, R.100 Ligand excluded by PLIP DMS.24: 4 residues within 4Å: Chain B: S.143, P.144, F.147 Ligands: DMS.19 Ligand excluded by PLIP DMS.25: 3 residues within 4Å: Chain B: G.68, T.69, R.70 Ligand excluded by PLIP DMS.26: 5 residues within 4Å: Chain B: S.297, S.299, S.301, A.302, D.305 Ligand excluded by PLIP DMS.36: 5 residues within 4Å: Chain B: H.357, M.361, E.364 Ligands: EDO.30, CL.40 Ligand excluded by PLIP

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

CL.7: 1 residues within 4Å: Chain A: L.193 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain A: A.167, G.170, H.204, A.206 Ligand excluded by PLIP CL.39: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.40: 2 residues within 4Å: Chain B: K.368 Ligands: DMS.36 Ligand excluded by PLIP

1 x KOU: (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-serine(Non-covalent)

KOU.27: 22 residues within 4Å: Chain B: H.86, K.87, T.110, G.111, A.112, G.113, Q.114, H.115, T.190, V.231, G.232, G.233, G.234, S.235, N.236, A.302, G.303, L.304, D.305, E.350, K.382 Ligands: DMS.15 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:Q.114 Hydrogen bonds: B:K.87, B:G.111, B:A.112, B:G.113, B:Q.114, 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:D.305 Water bridges: B:G.234, B:A.237 Salt bridges: B:H.86, B:K.87, B:K.87 pi-Stacking: B:H.86

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

PEG.28: 6 residues within 4Å: Chain A: S.180 Chain B: G.179, S.180, Y.181, E.182, T.183 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:S.180, A:S.180, B:E.182, B:T.183, B:T.183

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

EDO.29: 3 residues within 4Å: Chain B: P.23, Q.27, Y.181 3 PLIP interactions: 3 interactions with chain B Water bridges: B:P.23, B:Q.27, B:Y.181 EDO.30: 5 residues within 4Å: Chain B: I.253, D.323, V.325, H.357 Ligands: DMS.36 No protein-ligand interaction detected (PLIP) EDO.31: 5 residues within 4Å: Chain B: K.272, H.273, G.274 Ligands: DMS.12, DMS.18 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.273 EDO.32: 2 residues within 4Å: Chain B: G.320, D.323 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.323 Water bridges: B:R.321 EDO.33: 4 residues within 4Å: Chain B: A.46, D.47, K.50, N.51 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.46, B:N.51 Water bridges: B:D.47 EDO.34: 6 residues within 4Å: Chain B: G.10, E.11, F.12, Y.315, S.318, I.319 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.11, B:S.318 EDO.35: 5 residues within 4Å: Chain A: S.55 Chain B: S.163, I.294, E.296 Ligands: DMS.3 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Water bridges: A:S.55, B:E.296 Hydrogen bonds: B:E.296, B:E.296

2 x CS: CESIUM ION(Non-covalent)

CS.37: 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.16, H2O.20 CS.38: 7 residues within 4Å: Chain B: V.231, G.232, G.268, S.297, L.304, F.306, S.308 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:G.268

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hilario, E. et al., The external aldimine crystal structure of Salmonella typhimurium Tryptophan Synthase mutant beta-S377A in complex F9 inhibitor at the alpha-site and cesium ion at the metal coordination site. The single beta-Q114 rotamer conformation allows a hydrogen bond to form with the PLP oxygen at the position 3 in the ring. To be Published

Release Date

2021-08-25

Peptides

Tryptophan synthase alpha chain: A
Tryptophan synthase beta chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Tryptophan synthase alpha chain

Tryptophan synthase beta chain

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