SMTL ID : 6x0c.1

Tryptophan Synthase mutant beta-Q114A in complex with Cesium ion at the metal coordination site and aminoacrylate and benzimidazole at the enzyme beta site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

hetero-1-1-mer

Ligands

3 x BZI: BENZIMIDAZOLE(Non-covalent)

BZI.1: 7 residues within 4Å: Chain A: F.22, E.49, A.59, D.60, I.64, L.100, Y.175 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.22, A:I.64, A:L.100, A:L.100, A:Y.175 BZI.7: 5 residues within 4Å: Chain B: T.3, L.4, L.5, N.6, P.7 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:N.6 Hydrogen bonds: B:T.3 Water bridges: B:T.3 BZI.9: 10 residues within 4Å: Chain B: K.87, E.109, H.115, L.166, G.189, T.190, G.232, G.233, F.306 Ligands: 0JO.8 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.166, B:T.190 Hydrogen bonds: B:K.87, B:E.109 pi-Stacking: B:F.306

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

EDO.2: 4 residues within 4Å: Chain A: F.82, N.109, A.113, F.114 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.109, A:A.113 Water bridges: A:A.79, A:N.108 EDO.11: 5 residues within 4Å: Chain B: Q.36, E.203, R.206 Ligands: DMS.15, DMS.16 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.36, B:E.203 Water bridges: B:E.203, B:R.206

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

PEG.3: 6 residues within 4Å: Chain A: F.107, N.108, N.109, G.110 Chain B: R.275, V.276 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:V.276 Hydrogen bonds: A:G.110 PEG.10: 5 residues within 4Å: Chain B: L.59, T.60, K.61, Y.74, K.219 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:L.59, B:K.61 Water bridges: B:K.61, B:Q.63, B:E.343

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

DMS.4: 4 residues within 4Å: Chain A: N.147, I.148, A.149, R.171 No protein-ligand interaction detected (PLIP) DMS.12: 2 residues within 4Å: Chain B: Y.8, G.10 1 PLIP interactions: 1 interactions with chain B pi-Cation interactions: B:Y.8 DMS.13: 4 residues within 4Å: Chain B: K.50, G.54, R.55, P.56 No protein-ligand interaction detected (PLIP) DMS.14: 2 residues within 4Å: Chain B: L.271, N.317 1 PLIP interactions: 1 interactions with chain B Water bridges: B:N.317 DMS.15: 6 residues within 4Å: Chain B: Q.42, F.45, A.46, L.49, M.207 Ligands: EDO.11 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.46 DMS.16: 3 residues within 4Å: Chain B: Q.36, Q.42 Ligands: EDO.11 No protein-ligand interaction detected (PLIP)

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

CL.5: 4 residues within 4Å: Chain A: A.167, G.170, H.204, A.206 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: N.12, R.15, E.16 Ligand excluded by PLIP CL.19: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

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

0JO.8: 22 residues within 4Å: Chain B: A.85, H.86, K.87, T.110, G.111, G.113, A.114, H.115, 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 Ligands: BZI.9 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:A.85, B:E.350 Hydrogen bonds: B:H.86, B:T.110, B:G.111, B:A.112, B:G.113, B:A.114, B:H.115, B:G.232, B:G.233, B:G.234, B:S.235, B:S.235, B:N.236, B:N.236, B:S.377 Water bridges: B:A.237 Salt bridges: B:H.86, B:K.87, B:K.87 pi-Stacking: B:H.86

2 x CS: CESIUM ION(Non-covalent)

CS.17: 3 residues within 4Å: Chain B: T.66, T.69, T.71 No protein-ligand interaction detected (PLIP) CS.18: 6 residues within 4Å: Chain B: V.231, G.232, G.268, L.304, F.306, S.308 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:G.232, B:F.306

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hilario, E. et al., External aldimine form of Tryptophan Synthase mutant beta-Q114A in complex with Cesium ion at the metal coordination site and benzimidazole at the enzyme beta site. To be Published

Release Date

2021-03-10

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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