SMTL ID : 7k0b.1

The internal aldimine form of Salmonella typhimurium Tryptophan Synthase mutant beta-Q114A with cesium ion at the metal coordination site. A random beta-P270L mutation was inserted during PCR step

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.57 Å

Oligo State

hetero-1-1-mer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: P.28, G.29, A.74 Ligands: CL.14 1 PLIP interactions: 1 interactions with chain A Water bridges: A:P.28 EDO.2: 4 residues within 4Å: Chain A: N.66, L.69, R.70, A.73 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.70 EDO.4: 5 residues within 4Å: Chain A: L.34, K.35, D.38, L.87, K.91 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.38, A:K.91 EDO.5: 4 residues within 4Å: Chain A: S.221, A.264, A.265, R.267 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.267 EDO.16: 5 residues within 4Å: Chain B: C.170, Y.186, L.188, G.193, F.280 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.186 EDO.17: 4 residues within 4Å: Chain A: F.107, N.108 Chain B: R.275, V.276 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:V.276, A:F.107 Water bridges: B:R.275, A:G.110 EDO.18: 5 residues within 4Å: Chain B: I.65, T.66, A.67, T.69, M.362 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.65 EDO.20: 2 residues within 4Å: Chain B: R.131, D.176 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.176 Water bridges: B:R.131, B:R.131

1 x SER: SERINE(Non-covalent)

SER.3: 3 residues within 4Å: Chain A: P.217, S.257, F.258 No protein-ligand interaction detected (PLIP)

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

PEG.6: 7 residues within 4Å: Chain A: E.5, A.167, G.170, R.171, G.172, H.204, A.206 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.5, A:E.5, A:R.171, A:G.172 Water bridges: A:A.206

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

DMS.7: 7 residues within 4Å: Chain A: E.2, E.5, L.144, N.147, I.148, A.149, R.171 Ligand excluded by PLIP DMS.8: 4 residues within 4Å: Chain A: N.12, R.15, E.16, G.17 Ligand excluded by PLIP DMS.9: 5 residues within 4Å: Chain A: I.41, H.92, P.93, T.94, I.95 Ligand excluded by PLIP DMS.10: 5 residues within 4Å: Chain A: L.58, A.59 Chain B: P.18, I.20, S.178 Ligand excluded by PLIP DMS.11: 5 residues within 4Å: Chain A: A.59, D.60, L.100, I.153, Y.175 Ligand excluded by PLIP DMS.12: 2 residues within 4Å: Chain A: F.82, R.117 Ligand excluded by PLIP DMS.22: 4 residues within 4Å: Chain B: K.50, G.54, R.55, P.56 Ligand excluded by PLIP DMS.23: 2 residues within 4Å: Chain B: L.271, K.272 Ligand excluded by PLIP DMS.24: 5 residues within 4Å: Chain B: Q.42, F.45, A.46, L.49, M.207 Ligand excluded by PLIP DMS.25: 5 residues within 4Å: Chain B: Q.36, K.37, P.39, Q.42 Ligands: DMS.26 Ligand excluded by PLIP DMS.26: 3 residues within 4Å: Chain B: Q.36, Q.42 Ligands: DMS.25 Ligand excluded by PLIP DMS.27: 2 residues within 4Å: Chain B: P.56, Q.215 Ligand excluded by PLIP DMS.28: 2 residues within 4Å: Chain B: E.11, V.276 Ligand excluded by PLIP DMS.29: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP DMS.30: 4 residues within 4Å: Chain B: T.3, L.4, L.5, N.6 Ligand excluded by PLIP DMS.31: 1 residues within 4Å: Chain B: Y.8 Ligand excluded by PLIP DMS.32: 3 residues within 4Å: Chain B: Y.133, E.172, D.176 Ligand excluded by PLIP

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

CL.13: 5 residues within 4Å: Chain A: M.1, R.3, G.122, V.123, D.124 Ligand excluded by PLIP CL.14: 5 residues within 4Å: Chain A: G.29, I.30, E.31, Q.32 Ligands: EDO.1 Ligand excluded by PLIP CL.35: 4 residues within 4Å: Chain B: G.179, S.180, Y.181, E.182 Ligand excluded by PLIP CL.36: 2 residues within 4Å: Chain B: I.262, H.267 Ligand excluded by PLIP CL.37: 1 residues within 4Å: Chain B: D.218 Ligand excluded by PLIP CL.38: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.39: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

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

PLP.15: 17 residues within 4Å: Chain B: A.85, H.86, K.87, 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 18 PLIP interactions: 18 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.234, B:S.235, B:N.236, B:N.236, B:S.377 Water bridges: B:G.233, B:G.233, B:S.235, B:S.235, B:A.237 Salt bridges: B:H.86, B:K.87 pi-Stacking: B:H.86

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.19: 6 residues within 4Å: Chain B: L.5, F.32, Q.36, T.199, R.202, E.203 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.36, B:R.202, B:E.203

1 x BCN: BICINE(Non-covalent)

BCN.21: 13 residues within 4Å: Chain B: K.87, E.109, T.110, G.111, A.112, G.113, A.114, H.115, L.166, G.189, T.190, A.302, G.303 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:E.109, B:T.110, B:G.111, B:A.112, B:G.113, B:A.114, B:H.115, B:G.189 Water bridges: B:A.302 Salt bridges: B:K.87

2 x CS: CESIUM ION(Non-covalent)

CS.33: 3 residues within 4Å: Chain B: T.66, T.69, T.71 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.66 CS.34: 5 residues within 4Å: Chain B: V.231, G.232, E.256, G.268, S.308 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:G.232, B:E.256

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hilario, E. et al., The internal aldimine form of Salmonella typhimurium Tryptophan Synthase mutant beta-Q114A with cesium ion at the metal coordination site. A random beta-P270L mutation was inserted during PCR step. To be Published

Release Date

2021-09-22

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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