SMTL ID : 6wdu.1

The external aldimine form of the Salmonella thypi wild-type tryptophan synthase in open conformation showing multiple side chain conformations for the residue beta Q114 and sodium ion at the metal coordination site. One of the beta-Q114 rotamer conformations allows a hydrogen bond to form with the PLP oxygen at the position 3 in the ring.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

hetero-1-1-mer

Ligands

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

EDO.1: 3 residues within 4Å: Chain A: S.221, R.225, R.267 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.225, A:R.225 EDO.2: 1 residues within 4Å: Chain A: F.258 No protein-ligand interaction detected (PLIP) EDO.3: 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:T.94, A:I.95 EDO.8: 4 residues within 4Å: Chain B: P.56, M.207, E.211 Ligands: DMS.22 No protein-ligand interaction detected (PLIP) EDO.9: 3 residues within 4Å: Chain B: F.9, G.10, Y.315 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.10 Water bridges: B:Q.312 EDO.11: 3 residues within 4Å: Chain B: Q.36, Q.42 Ligands: DMS.20 2 PLIP interactions: 2 interactions with chain B Water bridges: B:Q.36, B:Q.36 EDO.12: 3 residues within 4Å: Chain B: K.219, E.220, G.221 2 PLIP interactions: 2 interactions with chain B Water bridges: B:L.217, B:D.218 EDO.15: 2 residues within 4Å: Chain B: E.210 Ligands: DMS.19 2 PLIP interactions: 2 interactions with chain B Water bridges: B:E.210, B:D.243

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

DMS.4: 3 residues within 4Å: Chain A: F.82, F.114, R.117 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.109 DMS.5: 4 residues within 4Å: Chain A: A.59, D.60, A.129, I.153 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:D.60 DMS.6: 5 residues within 4Å: Chain A: E.5, N.147, I.148, A.149, R.171 No protein-ligand interaction detected (PLIP) DMS.17: 5 residues within 4Å: Chain B: Q.42, F.45, A.46, L.49, M.207 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.46 DMS.18: 2 residues within 4Å: Chain B: R.363, E.364 No protein-ligand interaction detected (PLIP) DMS.19: 1 residues within 4Å: Ligands: EDO.15 No protein-ligand interaction detected (PLIP) DMS.20: 6 residues within 4Å: Chain B: Q.36, K.37, D.38, P.39, Q.42 Ligands: EDO.11 No protein-ligand interaction detected (PLIP) DMS.21: 4 residues within 4Å: Chain B: T.3, L.4, L.5, N.6 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.3 DMS.22: 5 residues within 4Å: Chain B: P.56, E.211, A.214, Q.215 Ligands: EDO.8 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.215 DMS.23: 3 residues within 4Å: Chain B: Y.8, G.10, E.11 3 PLIP interactions: 3 interactions with chain B Water bridges: B:Y.8 Salt bridges: B:E.11 pi-Cation interactions: B:Y.8 DMS.24: 3 residues within 4Å: Chain B: I.262, H.267, H.273 No protein-ligand interaction detected (PLIP) DMS.25: 2 residues within 4Å: Chain B: F.385, H.388 1 PLIP interactions: 1 interactions with chain B pi-Cation interactions: B:H.388 DMS.26: 8 residues within 4Å: Chain B: P.270, L.271, K.272, H.273, G.274, R.275, V.276, P.285 1 PLIP interactions: 1 interactions with chain B Water bridges: B:V.276 DMS.27: 6 residues within 4Å: Chain A: F.107, I.111, P.138, F.139 Chain B: Y.16, K.283 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.283

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

PEG.7: 3 residues within 4Å: Chain B: G.10, E.11, F.12 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.11 Water bridges: B:E.11 PEG.10: 6 residues within 4Å: Chain B: L.59, T.60, K.61, Q.63, Y.74, K.219 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.59, B:K.61 Water bridges: B:Y.74

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

NA.13: 4 residues within 4Å: Chain B: G.232, P.270, F.306, S.308 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.232 NA.14: 3 residues within 4Å: Chain B: T.66, T.69, T.71 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.69 Water bridges: B:T.66

1 x KOU: (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-serine(Non-covalent)

KOU.16: 23 residues within 4Å: Chain B: A.85, H.86, K.87, T.110, G.111, A.112, G.113, Q.114, H.115, T.190, C.230, V.231, G.232, G.233, G.234, S.235, N.236, A.302, G.303, L.304, D.305, E.350, S.377 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:A.85 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.233, B:G.234, B:S.235, B:N.236, B:N.236, B:D.305, B:S.377 Water bridges: B:E.109, B:Q.114, B:G.234, B:A.237, B:E.350 Salt bridges: B:H.86, B:K.87, B:K.87 pi-Stacking: B:H.86

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hilario, E. et al., The external aldimine form of the Salmonella thypi wild-type tryptophan synthase in open conformation showing multiple side chain conformations for the residue beta Q114 and sodium ion at the metal coordination site. One of the beta-Q114 rotamer conformations allows a hydrogen bond to form with the PLP oxygen at the position 3 in the ring. 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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