SMTL ID : 7kmc.1

The internal aldimine crystal structure of the beta-K167T mutant Tryptophan Synthase at 1.50 Angstrom resolution with cesium ion at the metal coordination site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

hetero-1-1-mer

Ligands

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

PEG.1: 4 residues within 4Å: Chain A: P.217, S.257, F.258, A.261 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.254 PEG.29: 9 residues within 4Å: Chain B: K.87, Q.114, G.189, T.190, G.303, F.306 Ligands: PLP.8, DMS.14, DMS.16 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.87, B:Q.114, B:G.303 Water bridges: B:T.190

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

DMS.2: 4 residues within 4Å: Chain A: S.221, V.224, R.225, A.268 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.225 DMS.3: 9 residues within 4Å: Chain A: M.1, R.3, E.119, V.123, D.124, H.146, N.147, I.148 Ligands: EDO.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:M.1 Water bridges: A:E.2, A:R.3 Salt bridges: A:D.124 DMS.9: 4 residues within 4Å: Chain B: K.50, G.54, R.55, P.56 No protein-ligand interaction detected (PLIP) DMS.10: 6 residues within 4Å: Chain B: Q.42, F.45, A.46, L.49, M.207 Ligands: EDO.27 No protein-ligand interaction detected (PLIP) DMS.11: 6 residues within 4Å: Chain B: H.273, G.274, R.275, M.286, M.287, Q.288 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.288 DMS.12: 3 residues within 4Å: Chain B: F.147, R.150, L.151 No protein-ligand interaction detected (PLIP) DMS.13: 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.14: 10 residues within 4Å: Chain B: T.190, A.192, G.232, G.233, F.280, M.282, F.306, S.308, V.309 Ligands: PEG.29 No protein-ligand interaction detected (PLIP) DMS.15: 3 residues within 4Å: Chain B: L.271, K.272, N.317 No protein-ligand interaction detected (PLIP) DMS.16: 7 residues within 4Å: Chain B: T.110, G.111, A.112, G.113, Q.114, H.115 Ligands: PEG.29 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.110, B:Q.114, B:H.115

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

CL.4: 2 residues within 4Å: Chain A: G.234, S.235 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain A: A.167, G.170, H.204, A.206 Ligand excluded by PLIP CL.17: 4 residues within 4Å: Chain B: T.3, L.4, L.5, N.6 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain B: G.127, L.128, K.129 Ligand excluded by PLIP CL.19: 2 residues within 4Å: Chain B: Q.36, K.37 Ligand excluded by PLIP CL.20: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.21: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

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

EDO.6: 3 residues within 4Å: Chain A: E.2, R.3 Ligands: DMS.3 3 PLIP interactions: 3 interactions with chain A Water bridges: A:E.2, A:R.3, A:D.124 EDO.7: 3 residues within 4Å: Chain A: D.112, A.113, A.116 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.112 Water bridges: A:D.112 EDO.22: 6 residues within 4Å: Chain B: N.64, I.65, T.338, H.342, M.362, R.363 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.363 EDO.23: 2 residues within 4Å: Chain B: F.385, H.388 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.388 EDO.24: 2 residues within 4Å: Chain B: K.272, H.273 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.272 EDO.25: 2 residues within 4Å: Chain B: A.290, D.291 No protein-ligand interaction detected (PLIP) EDO.26: 4 residues within 4Å: Chain B: I.262, E.263, G.265, H.267 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.263, B:H.267 EDO.27: 2 residues within 4Å: Chain B: A.46 Ligands: DMS.10 1 PLIP interactions: 1 interactions with chain B Water bridges: B:A.46 EDO.28: 7 residues within 4Å: Chain B: K.213, A.242, D.243, F.244, I.245, N.246, D.247 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:K.213, B:A.242, B:I.245, B:N.246 Water bridges: B:K.213, B:N.246, B:D.247

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

PLP.8: 18 residues within 4Å: Chain B: A.85, H.86, K.87, Q.114, T.190, C.230, V.231, G.232, G.233, G.234, S.235, N.236, G.303, A.348, E.350, S.377, G.378 Ligands: PEG.29 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:A.85, B:K.87, B:A.348 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:Q.114, 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

2 x CS: CESIUM ION(Non-covalent)

CS.30: 3 residues within 4Å: Chain B: T.66, T.69, T.71 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.71 CS.31: 6 residues within 4Å: Chain B: V.231, G.232, G.268, L.304, F.306, S.308 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hilario, E. et al., The internal aldimine crystal structure of the beta-K167T mutant Tryptophan Synthase at 1.50 Angstrom resolution with cesium ion at the metal coordination site. To be Published

Release Date

2021-11-03

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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