SMTL ID : 6dz4.1

Crystal structure of Salmonella typhimurium Tryptophan Synthase with sodium ion at the metal coordination site and (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-serine at the beta-site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

hetero-2-2-mer

Ligands

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

CL.1: 4 residues within 4Å: Chain A: H.92, P.93, T.94, I.95 Ligand excluded by PLIP CL.2: 1 residues within 4Å: Chain A: R.225 Ligand excluded by PLIP CL.10: 1 residues within 4Å: Chain B: R.150 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain B: K.219, E.220, G.221 Ligand excluded by PLIP CL.12: 1 residues within 4Å: Chain B: G.274 Ligand excluded by PLIP CL.13: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.14: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.15: 4 residues within 4Å: Chain A: I.111, P.138 Chain B: Y.16, K.283 Ligand excluded by PLIP CL.24: 4 residues within 4Å: Chain C: H.92, P.93, T.94, I.95 Ligand excluded by PLIP CL.25: 1 residues within 4Å: Chain C: R.225 Ligand excluded by PLIP CL.33: 1 residues within 4Å: Chain D: R.150 Ligand excluded by PLIP CL.34: 3 residues within 4Å: Chain D: K.219, E.220, G.221 Ligand excluded by PLIP CL.35: 1 residues within 4Å: Chain D: G.274 Ligand excluded by PLIP CL.36: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.37: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.38: 4 residues within 4Å: Chain C: I.111, P.138 Chain D: Y.16, K.283 Ligand excluded by PLIP

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

DMS.3: 3 residues within 4Å: Chain A: F.82, F.114, R.117 Ligand excluded by PLIP DMS.4: 5 residues within 4Å: Chain A: E.5, N.147, I.148, A.149, R.171 Ligand excluded by PLIP DMS.5: 4 residues within 4Å: Chain A: A.59, D.60, I.153, Y.175 Ligand excluded by PLIP DMS.6: 4 residues within 4Å: Chain A: N.12, E.16, G.17, V.224 Ligand excluded by PLIP DMS.16: 5 residues within 4Å: Chain B: Q.42, F.45, A.46, L.49, M.207 Ligand excluded by PLIP DMS.17: 2 residues within 4Å: Chain B: R.363, E.364 Ligand excluded by PLIP DMS.18: 6 residues within 4Å: Chain B: I.384, F.385, H.388 Chain D: S.143, P.144, F.147 Ligand excluded by PLIP DMS.19: 4 residues within 4Å: Chain B: I.262, G.265, H.267, H.273 Ligand excluded by PLIP DMS.20: 5 residues within 4Å: Chain B: Q.36, K.37, D.38, P.39, Q.42 Ligand excluded by PLIP DMS.21: 2 residues within 4Å: Chain B: Y.8, G.10 Ligand excluded by PLIP DMS.22: 4 residues within 4Å: Chain B: T.3, L.4, L.5, N.6 Ligand excluded by PLIP DMS.23: 4 residues within 4Å: Chain B: H.357, K.360, M.361, E.364 Ligand excluded by PLIP DMS.26: 3 residues within 4Å: Chain C: F.82, F.114, R.117 Ligand excluded by PLIP DMS.27: 5 residues within 4Å: Chain C: E.5, N.147, I.148, A.149, R.171 Ligand excluded by PLIP DMS.28: 4 residues within 4Å: Chain C: A.59, D.60, I.153, Y.175 Ligand excluded by PLIP DMS.29: 4 residues within 4Å: Chain C: N.12, E.16, G.17, V.224 Ligand excluded by PLIP DMS.39: 5 residues within 4Å: Chain D: Q.42, F.45, A.46, L.49, M.207 Ligand excluded by PLIP DMS.40: 2 residues within 4Å: Chain D: R.363, E.364 Ligand excluded by PLIP DMS.41: 6 residues within 4Å: Chain B: S.143, P.144, F.147 Chain D: I.384, F.385, H.388 Ligand excluded by PLIP DMS.42: 4 residues within 4Å: Chain D: I.262, G.265, H.267, H.273 Ligand excluded by PLIP DMS.43: 5 residues within 4Å: Chain D: Q.36, K.37, D.38, P.39, Q.42 Ligand excluded by PLIP DMS.44: 2 residues within 4Å: Chain D: Y.8, G.10 Ligand excluded by PLIP DMS.45: 4 residues within 4Å: Chain D: T.3, L.4, L.5, N.6 Ligand excluded by PLIP DMS.46: 4 residues within 4Å: Chain D: H.357, K.360, M.361, E.364 Ligand excluded by PLIP

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

KOU.7: 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 24 PLIP interactions: 24 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:G.234, B:A.237, B:E.350 Salt bridges: B:H.86, B:K.87, B:K.87 pi-Stacking: B:H.86 KOU.30: 23 residues within 4Å: Chain D: 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 26 PLIP interactions: 26 interactions with chain D Hydrophobic interactions: D:A.85 Hydrogen bonds: D:K.87, D:T.110, D:G.111, D:A.112, D:G.113, D:Q.114, D:H.115, D:G.232, D:G.233, D:G.234, D:S.235, D:N.236, D:N.236, D:D.305, D:S.377 Water bridges: D:E.109, D:T.190, D:T.190, D:G.234, D:A.237, D:E.350 Salt bridges: D:H.86, D:K.87, D:K.87 pi-Stacking: D:H.86

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

NA.8: 3 residues within 4Å: Chain B: T.66, T.69, T.71 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.66 Water bridges: B:T.66 NA.9: 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.31: 3 residues within 4Å: Chain D: T.66, T.69, T.71 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.66, D:T.71 NA.32: 4 residues within 4Å: Chain D: G.232, P.270, F.306, S.308 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.308

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hilario, E. et al., Crystal structure of Salmonella typhimurium Tryptophan Synthase with sodium ion at the metal coordination site and (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-serine at the beta site. To be Published

Release Date

2019-07-10

Peptides

Tryptophan synthase alpha chain: AC
Tryptophan synthase beta chain: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

Tryptophan synthase alpha chain

Tryptophan synthase beta chain

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