SMTL ID : 6vnt.1

Tryptophan synthase in complex with inhibitor N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the alpha-site, aminoacrylate at the beta site, and sodium ion at the metal coordination site at 1.25 Angstrom resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

hetero-2-2-mer

Ligands

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

EDO.1: 3 residues within 4Å: Chain A: R.15, V.224, A.268 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.16, A:G.227 EDO.4: 4 residues within 4Å: Chain B: H.260, T.328, D.330, E.331 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.260, B:D.330 Water bridges: B:E.331, B:E.331, B:E.331 EDO.5: 7 residues within 4Å: Chain B: T.60, K.61, C.62, Q.63, E.343 Chain D: Y.52, L.125 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.63 Water bridges: B:K.61 EDO.6: 5 residues within 4Å: Chain B: T.66, T.69, R.70, T.71, T.72 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.66 Water bridges: B:T.66, B:R.70, B:R.70, B:T.72 EDO.7: 3 residues within 4Å: Chain B: Y.8, G.10, E.11 1 PLIP interactions: 1 interactions with chain B Water bridges: B:G.10 EDO.11: 3 residues within 4Å: Chain C: R.15, V.224, A.268 2 PLIP interactions: 2 interactions with chain C Water bridges: C:E.16, C:G.227 EDO.14: 4 residues within 4Å: Chain D: H.260, T.328, D.330, E.331 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:H.260, D:T.328 Water bridges: D:E.331, D:E.331 EDO.15: 7 residues within 4Å: Chain B: Y.52, L.125 Chain D: T.60, K.61, C.62, Q.63, E.343 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Q.63, D:E.343 Water bridges: D:K.61 EDO.16: 5 residues within 4Å: Chain D: T.66, T.69, R.70, T.71, T.72 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:T.66, D:T.66, D:T.69 Water bridges: D:R.70, D:R.70 EDO.17: 3 residues within 4Å: Chain D: Y.8, G.10, E.11 1 PLIP interactions: 1 interactions with chain D Water bridges: D:G.10

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

F9F.2: 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 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.100, A:L.127, A:Y.175, A:T.183 Hydrogen bonds: A:R.179, A:G.184, A:F.212, A:G.213, A:I.214, A:G.234, A:S.235 Water bridges: A:I.214, A:I.214, A:A.236 pi-Stacking: A:F.212 F9F.12: 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 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:L.100, C:L.127, C:Y.175, C:T.183 Hydrogen bonds: C:Y.175, C:R.179, C:G.184, C:F.212, C:G.213, C:I.214, C:G.234, C:S.235 Water bridges: C:I.214, C:I.214, C:A.236 pi-Stacking: C:F.212

2 x 0JO: 2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid(Non-covalent)

0JO.3: 24 residues within 4Å: Chain B: A.85, H.86, K.87, T.110, G.111, A.112, G.113, Q.114, H.115, L.166, 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 28 PLIP interactions: 28 interactions with chain B Hydrophobic interactions: B:A.85, B:L.166, B:A.348, B:E.350 Hydrogen bonds: B:K.87, B:G.111, B:A.112, B:G.113, B:Q.114, B:H.115, B:T.190, B:G.232, B:G.234, B:S.235, B:S.235, B:N.236, B:N.236, B:S.377 Water bridges: B:K.87, B:K.87, B:E.109, B:G.233, B:A.237, B:G.303 Salt bridges: B:H.86, B:K.87, B:K.87 pi-Stacking: B:H.86 0JO.13: 24 residues within 4Å: Chain D: A.85, H.86, K.87, T.110, G.111, A.112, G.113, Q.114, H.115, L.166, 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 28 PLIP interactions: 28 interactions with chain D Hydrophobic interactions: D:A.85, D:L.166, D:A.348, D:E.350 Hydrogen bonds: D:K.87, D:T.110, D:G.111, D:A.112, D:G.113, D:Q.114, D:H.115, D:G.232, D:G.234, D:S.235, D:S.235, D:N.236, D:N.236, D:S.377 Water bridges: D:K.87, D:K.87, D:E.109, D:G.233, D:A.237, D:G.303 Salt bridges: D:H.86, D:K.87, D:K.87 pi-Stacking: D:H.86

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

NA.8: 7 residues within 4Å: Chain B: V.231, G.232, E.256, G.268, P.270, S.308, V.309 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.231 NA.18: 7 residues within 4Å: Chain D: V.231, G.232, E.256, G.268, P.270, S.308, V.309 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.256, D:G.268

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

PEG.9: 3 residues within 4Å: Chain B: E.211, A.214, Q.215 1 PLIP interactions: 1 interactions with chain B Water bridges: B:D.218 PEG.10: 4 residues within 4Å: Chain B: T.3, L.4, L.5, N.6 No protein-ligand interaction detected (PLIP) PEG.19: 3 residues within 4Å: Chain D: E.211, A.214, Q.215 1 PLIP interactions: 1 interactions with chain D Water bridges: D:D.218 PEG.20: 4 residues within 4Å: Chain D: T.3, L.4, L.5, N.6 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hilario, E. et al., Tryptophan synthase in complex with inhibitor N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the alpha-site, aminoacrylate at the beta site, and sodium ion at the metal coordination site at 1.25 Angstrom resolution. To be Published

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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