SMTL ID : 7jmq.1 (1 other biounit)

The external aldimine form of the mutant beta-S377A Salmonella thypi tryptophan synthase in open conformation showing dual side chain conformations for the residue beta-Q114, sodium ion at the metal coordination site, and F9 inhibitor at the alpha-site. One of the beta-Q114 rotamer conformations allows a hydrogen bond to form with the PLP oxygen at the position 3 in the ring

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

hetero-2-2-mer

Ligands

66 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: 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: 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, Q.210, A.222, A.226 Ligand excluded by PLIP DMS.5: 3 residues within 4Å: Chain A: F.82, F.114, R.117 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.7: 6 residues within 4Å: Chain A: N.12, R.15, E.16, G.17, V.224, A.268 Ligand excluded by PLIP DMS.9: 5 residues within 4Å: Chain A: M.1, N.147, I.148, A.149, R.171 Ligand excluded by PLIP DMS.10: 4 residues within 4Å: Chain A: E.31, L.34, E.83, L.87 Ligand excluded by PLIP DMS.11: 5 residues within 4Å: Chain A: R.179, S.180, G.181, N.187 Chain B: G.179 Ligand excluded by PLIP DMS.12: 4 residues within 4Å: Chain A: N.108, N.109 Chain B: R.275, A.290 Ligand excluded by PLIP DMS.14: 4 residues within 4Å: Chain B: Y.133, E.172, R.175, D.176 Ligand excluded by PLIP DMS.15: 8 residues within 4Å: Chain B: K.50, G.54, R.55, P.56 Chain D: P.56, T.57, Q.215 Ligands: DMS.58 Ligand excluded by PLIP DMS.16: 5 residues within 4Å: Chain B: Q.42, F.45, A.46, L.49, M.207 Ligand excluded by PLIP DMS.17: 5 residues within 4Å: Chain B: I.262, G.265, H.267, H.273 Ligands: DMS.18 Ligand excluded by PLIP DMS.18: 8 residues within 4Å: Chain B: H.273, G.274, R.275, M.286, M.287, Q.288, E.295 Ligands: DMS.17 Ligand excluded by PLIP DMS.20: 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.21: 4 residues within 4Å: Chain B: P.56, E.211, A.214, Q.215 Ligand excluded by PLIP DMS.22: 5 residues within 4Å: Chain A: S.180 Chain B: G.179, S.180, Y.181, E.182 Ligand excluded by PLIP DMS.23: 5 residues within 4Å: Chain B: S.143, V.146, F.147, R.150 Ligands: DMS.34 Ligand excluded by PLIP DMS.24: 4 residues within 4Å: Chain B: E.11, F.12, V.276, K.283 Ligand excluded by PLIP DMS.25: 6 residues within 4Å: Chain B: L.5, N.6, Y.8, F.9, H.195, T.199 Ligand excluded by PLIP DMS.26: 7 residues within 4Å: Chain B: P.270, L.271, K.272, H.273, G.274, V.276 Ligands: DMS.35 Ligand excluded by PLIP DMS.27: 4 residues within 4Å: Chain B: P.23, A.24, Q.27, Y.181 Ligand excluded by PLIP DMS.30: 2 residues within 4Å: Chain B: T.2, L.4 Ligand excluded by PLIP DMS.31: 8 residues within 4Å: Chain B: A.112, Q.114, Q.142, N.145, A.302, E.350, K.382, D.383 Ligand excluded by PLIP DMS.33: 6 residues within 4Å: Chain B: R.141, S.297, Y.298, S.299, S.301, D.305 Ligand excluded by PLIP DMS.34: 7 residues within 4Å: Chain B: S.143, P.144, F.147 Chain D: I.384, F.385, H.388 Ligands: DMS.23 Ligand excluded by PLIP DMS.35: 3 residues within 4Å: Chain B: L.271, N.317 Ligands: DMS.26 Ligand excluded by PLIP DMS.37: 6 residues within 4Å: Chain B: Q.36, K.37, D.38, P.39, Q.42 Ligands: DMS.40 Ligand excluded by PLIP DMS.38: 5 residues within 4Å: Chain B: F.147, R.150, L.151 Chain D: L.391, I.397 Ligand excluded by PLIP DMS.39: 2 residues within 4Å: Chain B: E.220, G.221 Ligand excluded by PLIP DMS.40: 3 residues within 4Å: Chain B: Q.36, Q.42 Ligands: DMS.37 Ligand excluded by PLIP DMS.44: 5 residues within 4Å: Chain C: I.41, H.92, P.93, T.94, I.95 Ligand excluded by PLIP DMS.45: 8 residues within 4Å: Chain C: V.128, V.131, S.136, F.139, R.140, P.150, I.151, F.152 Ligand excluded by PLIP DMS.46: 4 residues within 4Å: Chain C: S.55, L.69, F.72 Chain D: G.162 Ligand excluded by PLIP DMS.47: 6 residues within 4Å: Chain C: L.191, P.192, L.193, Q.210, A.222, A.226 Ligand excluded by PLIP DMS.48: 3 residues within 4Å: Chain C: F.82, F.114, R.117 Ligand excluded by PLIP DMS.49: 5 residues within 4Å: Chain C: L.34, K.35, D.38, L.87, K.91 Ligand excluded by PLIP DMS.50: 6 residues within 4Å: Chain C: N.12, R.15, E.16, G.17, V.224, A.268 Ligand excluded by PLIP DMS.52: 5 residues within 4Å: Chain C: M.1, N.147, I.148, A.149, R.171 Ligand excluded by PLIP DMS.53: 4 residues within 4Å: Chain C: E.31, L.34, E.83, L.87 Ligand excluded by PLIP DMS.54: 5 residues within 4Å: Chain C: R.179, S.180, G.181, N.187 Chain D: G.179 Ligand excluded by PLIP DMS.55: 4 residues within 4Å: Chain C: N.108, N.109 Chain D: R.275, A.290 Ligand excluded by PLIP DMS.57: 4 residues within 4Å: Chain D: Y.133, E.172, R.175, D.176 Ligand excluded by PLIP DMS.58: 8 residues within 4Å: Chain B: P.56, T.57, Q.215 Chain D: K.50, G.54, R.55, P.56 Ligands: DMS.15 Ligand excluded by PLIP DMS.59: 5 residues within 4Å: Chain D: Q.42, F.45, A.46, L.49, M.207 Ligand excluded by PLIP DMS.60: 5 residues within 4Å: Chain D: I.262, G.265, H.267, H.273 Ligands: DMS.61 Ligand excluded by PLIP DMS.61: 8 residues within 4Å: Chain D: H.273, G.274, R.275, M.286, M.287, Q.288, E.295 Ligands: DMS.60 Ligand excluded by PLIP DMS.63: 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.64: 4 residues within 4Å: Chain D: P.56, E.211, A.214, Q.215 Ligand excluded by PLIP DMS.65: 5 residues within 4Å: Chain C: S.180 Chain D: G.179, S.180, Y.181, E.182 Ligand excluded by PLIP DMS.66: 5 residues within 4Å: Chain D: S.143, V.146, F.147, R.150 Ligands: DMS.77 Ligand excluded by PLIP DMS.67: 4 residues within 4Å: Chain D: E.11, F.12, V.276, K.283 Ligand excluded by PLIP DMS.68: 6 residues within 4Å: Chain D: L.5, N.6, Y.8, F.9, H.195, T.199 Ligand excluded by PLIP DMS.69: 7 residues within 4Å: Chain D: P.270, L.271, K.272, H.273, G.274, V.276 Ligands: DMS.78 Ligand excluded by PLIP DMS.70: 4 residues within 4Å: Chain D: P.23, A.24, Q.27, Y.181 Ligand excluded by PLIP DMS.73: 2 residues within 4Å: Chain D: T.2, L.4 Ligand excluded by PLIP DMS.74: 8 residues within 4Å: Chain D: A.112, Q.114, Q.142, N.145, A.302, E.350, K.382, D.383 Ligand excluded by PLIP DMS.76: 6 residues within 4Å: Chain D: R.141, S.297, Y.298, S.299, S.301, D.305 Ligand excluded by PLIP DMS.77: 7 residues within 4Å: Chain B: I.384, F.385, H.388 Chain D: S.143, P.144, F.147 Ligands: DMS.66 Ligand excluded by PLIP DMS.78: 3 residues within 4Å: Chain D: L.271, N.317 Ligands: DMS.69 Ligand excluded by PLIP DMS.80: 6 residues within 4Å: Chain D: Q.36, K.37, D.38, P.39, Q.42 Ligands: DMS.83 Ligand excluded by PLIP DMS.81: 5 residues within 4Å: Chain B: L.391, I.397 Chain D: F.147, R.150, L.151 Ligand excluded by PLIP DMS.82: 2 residues within 4Å: Chain D: E.220, G.221 Ligand excluded by PLIP DMS.83: 3 residues within 4Å: Chain D: Q.36, Q.42 Ligands: DMS.80 Ligand excluded by PLIP

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

F9F.8: 19 residues within 4Å: Chain A: F.22, E.49, A.59, I.64, L.100, L.127, A.129, I.153, Y.175, L.177, T.183, G.184, F.212, G.213, I.232, S.233, G.234, S.235 Chain B: P.18 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.100, 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.51: 19 residues within 4Å: Chain C: F.22, E.49, A.59, I.64, L.100, L.127, A.129, I.153, Y.175, L.177, T.183, G.184, F.212, G.213, I.232, S.233, G.234, S.235 Chain D: P.18 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:L.100, 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

4 x CS: CESIUM ION(Non-covalent)

CS.13: 4 residues within 4Å: Chain A: A.167, G.170, H.204, A.206 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:A.167 CS.41: 3 residues within 4Å: Chain B: T.66, T.69, T.71 No protein-ligand interaction detected (PLIP) CS.56: 4 residues within 4Å: Chain C: A.167, G.170, H.204, A.206 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:A.167 CS.84: 3 residues within 4Å: Chain D: T.66, T.69, T.71 No protein-ligand interaction detected (PLIP)

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

KOU.19: 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: GOL.28 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:Q.114 Hydrogen bonds: B:K.87, B:T.110, B:G.111, B:A.112, B:G.113, B:Q.114, B:Q.114, B:H.115, B:G.232, B:G.233, B:G.234, B:S.235, B:N.236, B:N.236, B:D.305, B:E.350 Water bridges: B:T.190, B:T.190, B:G.234, B:A.237 Salt bridges: B:H.86, B:K.87, B:K.87 pi-Stacking: B:H.86 KOU.62: 22 residues within 4Å: Chain D: 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: GOL.71 22 PLIP interactions: 22 interactions with chain D Hydrophobic interactions: D:Q.114 Hydrogen bonds: D:K.87, D:G.111, D:A.112, D:G.113, D:Q.114, D:Q.114, D:H.115, D:T.190, D:G.232, D:G.233, D:G.234, D:S.235, D:N.236, D:N.236, D:D.305 Water bridges: D:G.234, D:A.237 Salt bridges: D:H.86, D:K.87, D:K.87 pi-Stacking: D:H.86

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.28: 10 residues within 4Å: Chain B: K.87, E.109, H.115, L.166, C.170, L.188, G.189, T.190, F.306 Ligands: KOU.19 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.109 Water bridges: B:G.303, B:F.306 GOL.29: 8 residues within 4Å: Chain B: L.59, T.60, K.61 Chain D: D.47, L.48, N.51, Y.52, L.125 10 PLIP interactions: 3 interactions with chain D, 7 interactions with chain B Hydrogen bonds: D:D.47, B:L.59, B:K.61 Water bridges: D:N.51, D:N.51, B:K.61, B:K.61, B:Q.63, B:Q.63, B:E.343 GOL.71: 10 residues within 4Å: Chain D: K.87, E.109, H.115, L.166, C.170, L.188, G.189, T.190, F.306 Ligands: KOU.62 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:E.109, D:E.109 Water bridges: D:G.303, D:F.306 GOL.72: 8 residues within 4Å: Chain B: D.47, L.48, N.51, Y.52, L.125 Chain D: L.59, T.60, K.61 10 PLIP interactions: 7 interactions with chain D, 3 interactions with chain B Hydrogen bonds: D:L.59, D:K.61, B:D.47 Water bridges: D:K.61, D:K.61, D:Q.63, D:Q.63, D:E.343, B:N.51, B:N.51

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

EDO.32: 5 residues within 4Å: Chain B: P.158, V.159, H.160, S.161, E.172 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.160, B:S.161 Water bridges: B:S.161, B:E.172, B:E.172 EDO.36: 2 residues within 4Å: Chain B: K.99, R.100 2 PLIP interactions: 2 interactions with chain B Water bridges: B:K.99, B:R.100 EDO.75: 5 residues within 4Å: Chain D: P.158, V.159, H.160, S.161, E.172 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:H.160, D:S.161 Water bridges: D:S.161, D:E.172 EDO.79: 2 residues within 4Å: Chain D: K.99, R.100 2 PLIP interactions: 2 interactions with chain D Water bridges: D:K.99, D:R.100

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

NA.42: 6 residues within 4Å: Chain B: V.231, G.232, E.256, G.268, P.270, S.308 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.256, B:S.308 NA.85: 6 residues within 4Å: Chain D: V.231, G.232, E.256, G.268, P.270, S.308 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.232

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

CL.43: 1 residues within 4Å: Chain B: Y.8 Ligand excluded by PLIP CL.86: 1 residues within 4Å: Chain D: Y.8 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hilario, E. et al., The external aldimine form of mutant beta-S377A Salmonella thypi tryptophan synthase in open conformation showing dual side chain conformations for the residue beta-Q114, sodium ion at the metal coordination site, and F9 inhibitor at the alpha-site. One of the beta-Q114 rotamer conformations allows a hydrogen bond to form with the PLP oxygen at the position 3 in the ring. 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

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