SMTL ID : 6vfd.1

Tryptophan synthase mutant Q114A in complex with cesium ion at the metal coordination site and 2-aminophenol quinonoid at the enzyme beta site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-2-2-mer

Ligands

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

EDO.1: 5 residues within 4Å: Chain A: F.107, N.108, G.110 Chain B: R.275, V.276 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:R.275, B:V.276, A:G.110 Water bridges: B:Q.288, A:N.108, A:N.109, A:I.111 EDO.2: 5 residues within 4Å: Chain A: F.22, E.49, I.64, Y.175, G.234 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.175, A:Y.175 EDO.9: 4 residues within 4Å: Chain B: T.289, A.290, D.291, Q.293 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.289, B:A.290, B:D.291, B:D.291 Water bridges: B:D.291 EDO.10: 3 residues within 4Å: Chain B: K.219, E.220 Ligands: CL.36 2 PLIP interactions: 2 interactions with chain B Water bridges: B:E.220, B:E.220 EDO.37: 5 residues within 4Å: Chain C: F.107, N.108, G.110 Chain D: R.275, V.276 7 PLIP interactions: 3 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:R.275, D:V.276, C:G.110 Water bridges: D:Q.288, C:N.108, C:N.109, C:I.111 EDO.38: 5 residues within 4Å: Chain C: F.22, E.49, I.64, Y.175, G.234 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.175 EDO.45: 4 residues within 4Å: Chain D: T.289, A.290, D.291, Q.293 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:T.289, D:A.290, D:D.291 Water bridges: D:D.291 EDO.46: 3 residues within 4Å: Chain D: K.219, E.220 Ligands: CL.72 2 PLIP interactions: 2 interactions with chain D Water bridges: D:E.220, D:E.220

4 x SER: SERINE(Non-covalent)

SER.3: 4 residues within 4Å: Chain A: F.82, A.113, F.114, R.117 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:F.114, S.3, S.3 Water bridges: A:A.79, A:N.108 SER.8: 4 residues within 4Å: Chain B: Y.8, F.9, G.10, Y.315 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.8, B:G.10 Water bridges: B:G.10 SER.39: 4 residues within 4Å: Chain C: F.82, A.113, F.114, R.117 5 PLIP interactions: 2 Ligand-Ligand interactions, 3 interactions with chain C Hydrogen bonds: S.39, S.39, C:F.114 Water bridges: C:A.79, C:N.108 SER.44: 4 residues within 4Å: Chain D: Y.8, F.9, G.10, Y.315 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Y.8, D:G.10, D:Y.315 Water bridges: D:G.10

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

DMS.4: 5 residues within 4Å: Chain A: I.41, H.92, P.93, T.94, I.95 Ligand excluded by PLIP DMS.11: 4 residues within 4Å: Chain B: I.262, G.265, H.267, H.273 Ligand excluded by PLIP DMS.12: 1 residues within 4Å: Chain B: E.331 Ligand excluded by PLIP DMS.13: 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.14: 2 residues within 4Å: Chain B: Y.8, G.10 Ligand excluded by PLIP DMS.15: 10 residues within 4Å: Chain B: K.50, G.54, R.55, P.56 Chain D: P.56, T.57, A.58, Q.215 Ligands: CS.22, CS.58 Ligand excluded by PLIP DMS.16: 3 residues within 4Å: Chain B: L.271, K.272, N.317 Ligand excluded by PLIP DMS.17: 5 residues within 4Å: Chain B: Q.42, F.45, A.46, L.49, M.207 Ligand excluded by PLIP DMS.18: 4 residues within 4Å: Chain B: T.3, L.4, L.5, N.6 Ligand excluded by PLIP DMS.19: 4 residues within 4Å: Chain B: P.56, E.211, A.214, Q.215 Ligand excluded by PLIP DMS.40: 5 residues within 4Å: Chain C: I.41, H.92, P.93, T.94, I.95 Ligand excluded by PLIP DMS.47: 4 residues within 4Å: Chain D: I.262, G.265, H.267, H.273 Ligand excluded by PLIP DMS.48: 1 residues within 4Å: Chain D: E.331 Ligand excluded by PLIP DMS.49: 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.50: 2 residues within 4Å: Chain D: Y.8, G.10 Ligand excluded by PLIP DMS.51: 10 residues within 4Å: Chain B: P.56, T.57, A.58, Q.215 Chain D: K.50, G.54, R.55, P.56 Ligands: CS.22, CS.58 Ligand excluded by PLIP DMS.52: 3 residues within 4Å: Chain D: L.271, K.272, N.317 Ligand excluded by PLIP DMS.53: 5 residues within 4Å: Chain D: Q.42, F.45, A.46, L.49, M.207 Ligand excluded by PLIP DMS.54: 4 residues within 4Å: Chain D: T.3, L.4, L.5, N.6 Ligand excluded by PLIP DMS.55: 4 residues within 4Å: Chain D: P.56, E.211, A.214, Q.215 Ligand excluded by PLIP

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

CL.5: 3 residues within 4Å: Chain A: A.167, G.170, H.204 Ligand excluded by PLIP CL.6: 1 residues within 4Å: Chain A: I.153 Ligand excluded by PLIP CL.23: 2 residues within 4Å: Chain B: Q.36, Q.42 Ligand excluded by PLIP CL.24: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.25: 2 residues within 4Å: Chain B: D.225, S.249 Ligand excluded by PLIP CL.26: 3 residues within 4Å: Chain B: H.273, G.274, R.275 Ligand excluded by PLIP CL.27: 1 residues within 4Å: Chain B: H.357 Ligand excluded by PLIP CL.28: 2 residues within 4Å: Chain B: I.319, R.321 Ligand excluded by PLIP CL.29: 2 residues within 4Å: Chain B: R.150, L.151 Ligand excluded by PLIP CL.30: 1 residues within 4Å: Chain B: E.155 Ligand excluded by PLIP CL.31: 1 residues within 4Å: Chain B: H.342 Ligand excluded by PLIP CL.32: 2 residues within 4Å: Chain B: Q.36, K.37 Ligand excluded by PLIP CL.33: 2 residues within 4Å: Chain B: K.368, E.369 Ligand excluded by PLIP CL.34: 2 residues within 4Å: Chain B: T.248, G.251 Ligand excluded by PLIP CL.35: 1 residues within 4Å: Chain B: E.172 Ligand excluded by PLIP CL.36: 5 residues within 4Å: Chain B: D.218, K.219, E.220, G.221 Ligands: EDO.10 Ligand excluded by PLIP CL.41: 3 residues within 4Å: Chain C: A.167, G.170, H.204 Ligand excluded by PLIP CL.42: 1 residues within 4Å: Chain C: I.153 Ligand excluded by PLIP CL.59: 2 residues within 4Å: Chain D: Q.36, Q.42 Ligand excluded by PLIP CL.60: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.61: 2 residues within 4Å: Chain D: D.225, S.249 Ligand excluded by PLIP CL.62: 3 residues within 4Å: Chain D: H.273, G.274, R.275 Ligand excluded by PLIP CL.63: 1 residues within 4Å: Chain D: H.357 Ligand excluded by PLIP CL.64: 2 residues within 4Å: Chain D: I.319, R.321 Ligand excluded by PLIP CL.65: 2 residues within 4Å: Chain D: R.150, L.151 Ligand excluded by PLIP CL.66: 1 residues within 4Å: Chain D: E.155 Ligand excluded by PLIP CL.67: 1 residues within 4Å: Chain D: H.342 Ligand excluded by PLIP CL.68: 2 residues within 4Å: Chain D: Q.36, K.37 Ligand excluded by PLIP CL.69: 2 residues within 4Å: Chain D: K.368, E.369 Ligand excluded by PLIP CL.70: 2 residues within 4Å: Chain D: T.248, G.251 Ligand excluded by PLIP CL.71: 1 residues within 4Å: Chain D: E.172 Ligand excluded by PLIP CL.72: 5 residues within 4Å: Chain D: D.218, K.219, E.220, G.221 Ligands: EDO.46 Ligand excluded by PLIP

2 x 1D0: (2E)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)imino]-3-[(2-hydroxyphenyl)amino]propanoic acid(Non-covalent)

1D0.7: 24 residues within 4Å: Chain B: A.85, H.86, K.87, E.109, T.110, G.111, A.112, G.113, A.114, H.115, T.190, C.230, V.231, G.232, G.233, G.234, S.235, N.236, G.303, L.304, F.306, E.350, S.377, G.378 27 PLIP interactions: 27 interactions with chain B Hydrophobic interactions: B:A.85, B:T.190, B:E.350 Hydrogen bonds: B:K.87, B:E.109, B:T.110, B:G.111, B:A.112, B:G.113, B:A.114, B:H.115, B:T.190, B:G.232, B:G.233, B:G.234, B:S.235, B:S.235, B:N.236, B:N.236, B:S.377 Water bridges: B:G.234, B:A.237 Salt bridges: B:H.86, B:K.87, B:K.87 pi-Stacking: B:H.86, B:F.306 1D0.43: 24 residues within 4Å: Chain D: A.85, H.86, K.87, E.109, T.110, G.111, A.112, G.113, A.114, H.115, T.190, C.230, V.231, G.232, G.233, G.234, S.235, N.236, G.303, L.304, F.306, E.350, S.377, G.378 27 PLIP interactions: 27 interactions with chain D Hydrophobic interactions: D:A.85, D:T.190, D:E.350 Hydrogen bonds: D:K.87, D:E.109, D:E.109, D:G.111, D:A.112, D:G.113, D:A.114, D:H.115, D:T.190, D:G.232, D:G.233, D:G.234, D:S.235, D:S.235, D:N.236, D:N.236, D:S.377 Water bridges: D:G.234, D:A.237 Salt bridges: D:H.86, D:K.87, D:K.87 pi-Stacking: D:H.86, D:F.306

6 x CS: CESIUM ION(Non-covalent)

CS.20: 3 residues within 4Å: Chain B: T.66, T.69, T.71 No protein-ligand interaction detected (PLIP) CS.21: 6 residues within 4Å: Chain B: V.231, G.232, G.268, 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 CS.22: 7 residues within 4Å: Chain B: G.54, P.56 Chain D: G.54, P.56 Ligands: DMS.15, DMS.51, CS.58 No protein-ligand interaction detected (PLIP) CS.56: 3 residues within 4Å: Chain D: T.66, T.69, T.71 No protein-ligand interaction detected (PLIP) CS.57: 6 residues within 4Å: Chain D: V.231, G.232, G.268, L.304, F.306, S.308 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:G.232, D:G.268, D:F.306 CS.58: 7 residues within 4Å: Chain B: G.54, P.56 Chain D: G.54, P.56 Ligands: DMS.15, CS.22, DMS.51 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hilario, E. et al., Tryptophan synthase mutant Q114A in complex with cesium ion at the metal coordination site and 2-aminophenol quinonoid at the enzyme beta site. To be Published

Release Date

2020-08-05

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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