SMTL ID : 7kh6.1

1.45 Angstrom resolution internal aldimine crystal structure of the beta-Q114A mutant of TryptophanSynthase in complex with N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the enzyme alpha-site and cesium ion at the metal coordination site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

hetero-1-1-mer

Ligands

13 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 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.94, A:I.95 Water bridges: A:H.92 DMS.2: 9 residues within 4Å: Chain A: Y.115, V.128, V.131, S.136, F.139, R.140, P.150, I.151, F.152 No protein-ligand interaction detected (PLIP) DMS.3: 9 residues within 4Å: Chain A: M.1, R.3, E.119, G.122, V.123, D.124, H.146, N.147, I.148 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.1 Water bridges: A:R.3 Salt bridges: A:D.124 DMS.4: 7 residues within 4Å: Chain A: L.191, P.192, L.193, H.194, Q.210, A.222, A.226 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.193 Water bridges: A:H.194 DMS.5: 3 residues within 4Å: Chain A: F.82, F.114, R.117 No protein-ligand interaction detected (PLIP) DMS.6: 4 residues within 4Å: Chain A: N.12, R.15, E.16, V.224 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.17 DMS.7: 5 residues within 4Å: Chain A: L.144, N.147, I.148, A.149, R.171 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.5 DMS.13: 4 residues within 4Å: Chain B: Y.133, E.172, R.175, D.176 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:E.172, B:D.176 DMS.14: 4 residues within 4Å: Chain B: K.50, G.54, R.55, P.56 No protein-ligand interaction detected (PLIP) DMS.15: 5 residues within 4Å: Chain B: Q.42, F.45, A.46, L.49, M.207 No protein-ligand interaction detected (PLIP) DMS.16: 4 residues within 4Å: Chain B: I.262, G.265, H.267, H.273 No protein-ligand interaction detected (PLIP) DMS.17: 4 residues within 4Å: Chain B: T.3, L.4, L.5, N.6 No protein-ligand interaction detected (PLIP) DMS.18: 4 residues within 4Å: Chain B: Q.36, K.37, Q.42 Ligands: EDO.19 No protein-ligand interaction detected (PLIP)

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

F9F.8: 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:I.153, 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

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

EDO.9: 3 residues within 4Å: Chain A: P.217, F.258, A.261 No protein-ligand interaction detected (PLIP) EDO.19: 3 residues within 4Å: Chain B: Q.36, Q.42 Ligands: DMS.18 2 PLIP interactions: 2 interactions with chain B Water bridges: B:Q.36, B:Q.42 EDO.20: 3 residues within 4Å: Chain B: L.271, K.272, N.317 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.271, B:N.317 EDO.21: 4 residues within 4Å: Chain B: D.218, K.219, E.220, G.221 1 PLIP interactions: 1 interactions with chain B Water bridges: B:L.217

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

CL.10: 3 residues within 4Å: Chain A: A.167, G.170, H.204 Ligand excluded by PLIP CL.25: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.26: 1 residues within 4Å: Chain B: E.369 Ligand excluded by PLIP

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

PEG.11: 8 residues within 4Å: Chain A: F.107, I.111, E.135, P.138, F.139 Chain B: Y.8, Y.16, K.283 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.16, B:K.283 Water bridges: B:Y.8, B:Y.8

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

PLP.12: 17 residues within 4Å: Chain B: A.85, H.86, K.87, A.114, T.190, C.230, V.231, G.232, G.233, G.234, S.235, N.236, G.303, L.304, E.350, S.377, G.378 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:A.85, B:K.87 Hydrogen bonds: B:T.190, B:G.232, B:G.233, B:G.234, B:S.235, B:N.236, B:N.236, B:S.377 Water bridges: B:T.190, B:T.190, B:S.235, B:S.235, B:A.237 Salt bridges: B:H.86, B:K.87 pi-Stacking: B:H.86

3 x CS: CESIUM ION(Non-covalent)(Non-functional Binders)

CS.22: 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.23: 3 residues within 4Å: Chain B: T.66, T.69, T.71 No protein-ligand interaction detected (PLIP) CS.24: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hilario, E. et al., 1.45 Angstrom resolution internal aldimine crystal structure of the beta-Q114A mutant of TryptophanSynthase in complex with N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the enzyme alpha-site and cesium ion at the metal coordination site. To be Published

Release Date

2021-10-27

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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