SMTL ID : 7jqw.1

The external aldimine crystal structure of Salmonella typhimurium Tryptophan Synthase mutant beta-S377A in complex with cesium ion at the metal coordination site. The single beta-Q114 rotamer conformation allows a hydrogen bond to form with the PLP oxygen at the position 3 in the ring

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-1-1-mer

Ligands

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

DMS.1: 8 residues within 4Å: Chain A: R.3, E.119, G.122, V.123, D.124, H.146, N.147, I.148 Ligand excluded by PLIP DMS.2: 6 residues within 4Å: Chain A: P.78, F.82, L.105, N.108, N.109 Chain B: D.291 Ligand excluded by PLIP DMS.3: 9 residues within 4Å: Chain A: Y.115, V.128, V.131, S.136, F.139, R.140, P.150, I.151, F.152 Ligand excluded by PLIP DMS.4: 4 residues within 4Å: Chain A: R.164, A.167, S.168, Y.203 Ligand excluded by PLIP DMS.5: 5 residues within 4Å: Chain A: I.64, F.212, G.213, G.234, S.235 Ligand excluded by PLIP DMS.11: 4 residues within 4Å: Chain B: K.50, G.54, R.55, P.56 Ligand excluded by PLIP DMS.12: 4 residues within 4Å: Chain B: F.41, Q.44, L.96, R.100 Ligand excluded by PLIP DMS.13: 3 residues within 4Å: Chain B: T.60, K.61, Q.63 Ligand excluded by PLIP DMS.14: 8 residues within 4Å: Chain B: A.112, Q.114, Q.142, N.145, A.302, E.350, K.382, D.383 Ligand excluded by PLIP DMS.15: 7 residues within 4Å: Chain B: P.270, L.271, K.272, H.273, G.274, P.285 Ligands: EDO.26 Ligand excluded by PLIP DMS.16: 8 residues within 4Å: Chain B: S.123, A.124, L.128, K.129, C.130, M.152, G.153, A.154 Ligand excluded by PLIP DMS.17: 6 residues within 4Å: Chain B: K.87, E.109, L.166, G.189, T.190 Ligands: KOU.25 Ligand excluded by PLIP DMS.18: 4 residues within 4Å: Chain A: N.108, N.109 Chain B: R.275, A.290 Ligand excluded by PLIP DMS.19: 8 residues within 4Å: Chain B: H.267, H.273, G.274, M.286, M.287, Q.288, E.295 Ligands: DMS.20 Ligand excluded by PLIP DMS.20: 5 residues within 4Å: Chain B: I.262, G.265, H.267, H.273 Ligands: DMS.19 Ligand excluded by PLIP DMS.21: 3 residues within 4Å: Chain B: N.64, R.341, H.342 Ligand excluded by PLIP DMS.22: 3 residues within 4Å: Chain B: Q.42, F.45, A.46 Ligand excluded by PLIP DMS.24: 4 residues within 4Å: Chain B: N.6, Y.8, F.9, T.199 Ligand excluded by PLIP

2 x 2AF: 2-AMINOPHENOL(Non-covalent)

2AF.6: 9 residues within 4Å: Chain A: E.134, P.155, N.157, A.158, D.159, L.162 Chain B: Q.19, M.22, P.23 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:N.157, A:N.157, A:D.159 Hydrophobic interactions: B:Q.19, B:M.22, B:P.23 2AF.23: 6 residues within 4Å: Chain B: H.82, G.83, V.117, L.121, R.148, R.379 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.117, B:L.121 Hydrogen bonds: B:R.379 Water bridges: B:G.83

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

CL.7: 2 residues within 4Å: Chain A: F.107, I.111 Ligand excluded by PLIP CL.8: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain A: A.167, G.170, R.171, H.204 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain A: T.94, I.95 Ligand excluded by PLIP CL.28: 4 residues within 4Å: Chain B: G.259, T.328, D.329, D.330 Ligand excluded by PLIP CL.29: 3 residues within 4Å: Chain B: Q.312, Y.315, L.316 Ligand excluded by PLIP CL.30: 1 residues within 4Å: Chain B: R.321 Ligand excluded by PLIP CL.31: 3 residues within 4Å: Chain B: Q.36, K.37, P.39 Ligand excluded by PLIP CL.32: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.33: 4 residues within 4Å: Chain B: E.11, F.12, Y.315, S.318 Ligand excluded by PLIP CL.34: 5 residues within 4Å: Chain B: R.222, L.223, P.224, D.225, S.249 Ligand excluded by PLIP CL.35: 3 residues within 4Å: Chain B: S.297, S.299, D.305 Ligand excluded by PLIP

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

KOU.25: 23 residues within 4Å: Chain B: 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, K.382 Ligands: DMS.17 24 PLIP interactions: 24 interactions with chain B Hydrogen bonds: B:K.87, B:T.110, B:G.111, B:A.112, B:G.113, B:Q.114, B:Q.114, B:H.115, B:G.232, B:G.233, B:G.234, B:S.235, B:N.236, B:N.236, B:D.305, B:E.350 Water bridges: B:T.190, B:T.190, B:G.234, B:A.237 Salt bridges: B:H.86, B:K.87, B:K.87 pi-Stacking: B:H.86

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

EDO.26: 4 residues within 4Å: Chain B: F.12, V.276, S.318 Ligands: DMS.15 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.317, B:S.318 Water bridges: B:V.276

1 x SER: SERINE(Non-covalent)

SER.27: 5 residues within 4Å: Chain B: K.129, R.150, G.153, A.154, E.155 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: B:K.129, B:G.153 Water bridges: B:G.153, B:V.156, S.27

2 x CS: CESIUM ION(Non-covalent)

CS.36: 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.37: 7 residues within 4Å: Chain B: V.231, G.232, G.268, P.270, L.304, F.306, S.308 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:G.232, B:G.268, B:F.306

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hilario, E. et al., The external aldimine crystal structure of Salmonella typhimurium Tryptophan Synthase mutant beta-S377A in complex with cesium ion at the metal coordination site. The single beta-Q114 rotamer conformation allows a hydrogen bond to form with the PLP oxygen at the position 3 in the ring. To be Published

Release Date

2021-08-25

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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