SMTL ID : 6o1h.1

Tryptophan synthase Q114A mutant in complex with N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the enzyme alpha-site, cesium ion at the metal coordination site, and 2-aminophenol quinonoid at the enzyme beta site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.64 Å

Oligo State

hetero-2-2-mer

Ligands

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

DMS.1: 9 residues within 4Å: Chain A: M.1, R.3, E.119, G.122, V.123, D.124, H.146, N.147, I.148 Ligand excluded by PLIP DMS.2: 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: 5 residues within 4Å: Chain A: M.1, N.147, I.148, A.149, R.171 Ligand excluded by PLIP DMS.9: 8 residues within 4Å: Chain B: P.55, T.56, A.57, Q.214 Chain D: K.49, G.53, R.54, P.55 Ligand excluded by PLIP DMS.10: 5 residues within 4Å: Chain A: S.180 Chain B: G.178, S.179, Y.180, E.181 Ligand excluded by PLIP DMS.11: 4 residues within 4Å: Chain B: Q.41, F.44, A.45, L.48 Ligand excluded by PLIP DMS.13: 4 residues within 4Å: Chain B: Y.132, E.171, R.174, D.175 Ligand excluded by PLIP DMS.14: 1 residues within 4Å: Chain B: E.330 Ligand excluded by PLIP DMS.31: 9 residues within 4Å: Chain C: M.1, R.3, E.119, G.122, V.123, D.124, H.146, N.147, I.148 Ligand excluded by PLIP DMS.32: 9 residues within 4Å: Chain C: Y.115, V.128, V.131, S.136, F.139, R.140, P.150, I.151, F.152 Ligand excluded by PLIP DMS.34: 5 residues within 4Å: Chain C: M.1, N.147, I.148, A.149, R.171 Ligand excluded by PLIP DMS.39: 8 residues within 4Å: Chain B: K.49, G.53, R.54, P.55 Chain D: P.55, T.56, A.57, Q.214 Ligand excluded by PLIP DMS.40: 5 residues within 4Å: Chain C: S.180 Chain D: G.178, S.179, Y.180, E.181 Ligand excluded by PLIP DMS.41: 4 residues within 4Å: Chain D: Q.41, F.44, A.45, L.48 Ligand excluded by PLIP DMS.43: 4 residues within 4Å: Chain D: Y.132, E.171, R.174, D.175 Ligand excluded by PLIP DMS.44: 1 residues within 4Å: Chain D: E.330 Ligand excluded by PLIP

2 x F9F: 2-({[4-(TRIFLUOROMETHOXY)PHENYL]SULFONYL}AMINO)ETHYL DIHYDROGEN PHOSPHATE(Non-covalent)

F9F.3: 18 residues within 4Å: Chain A: F.22, E.49, A.59, I.64, L.100, L.127, A.129, I.153, Y.175, T.183, G.184, F.212, G.213, I.232, S.233, G.234, S.235 Chain B: P.17 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.100, A:L.127, A:Y.175, A:T.183 Hydrogen bonds: A:Y.175, A:R.179, A:G.184, A:F.212, A:G.213, A:G.234, A:S.235 Water bridges: A:F.212, A:I.214, A:A.236 pi-Stacking: A:F.212 F9F.33: 18 residues within 4Å: Chain C: F.22, E.49, A.59, I.64, L.100, L.127, A.129, I.153, Y.175, T.183, G.184, F.212, G.213, I.232, S.233, G.234, S.235 Chain D: P.17 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:L.100, C:L.127, C:Y.175, C:T.183 Hydrogen bonds: C:R.179, C:G.184, C:F.212, C:G.213, C:G.234, C:S.235 Water bridges: C:F.212, C:I.214, C:A.236 pi-Stacking: C:F.212

6 x CS: CESIUM ION(Non-covalent)

CS.5: 4 residues within 4Å: Chain A: A.167, G.170, H.204, A.206 No protein-ligand interaction detected (PLIP) CS.15: 3 residues within 4Å: Chain B: T.65, T.68, T.70 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.70 CS.16: 6 residues within 4Å: Chain B: V.230, G.231, G.267, L.303, F.305, S.307 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:G.231, B:G.267, B:F.305 CS.35: 4 residues within 4Å: Chain C: A.167, G.170, H.204, A.206 No protein-ligand interaction detected (PLIP) CS.45: 3 residues within 4Å: Chain D: T.65, T.68, T.70 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.70 CS.46: 6 residues within 4Å: Chain D: V.230, G.231, G.267, L.303, F.305, S.307 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:G.231, D:G.267, D:F.305

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

CL.6: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: R.179, S.180, G.181 Ligand excluded by PLIP CL.17: 1 residues within 4Å: Chain B: A.213 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain B: A.30, S.33, R.99 Ligand excluded by PLIP CL.19: 2 residues within 4Å: Chain B: Q.35, Q.41 Ligand excluded by PLIP CL.20: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.21: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.22: 1 residues within 4Å: Chain B: F.8 Ligand excluded by PLIP CL.23: 2 residues within 4Å: Chain B: V.324, S.325 Ligand excluded by PLIP CL.24: 4 residues within 4Å: Chain B: T.247, V.249, G.250, R.320 Ligand excluded by PLIP CL.25: 3 residues within 4Å: Chain A: P.57 Chain B: N.170, R.174 Ligand excluded by PLIP CL.26: 1 residues within 4Å: Chain D: R.149 Ligand excluded by PLIP CL.27: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.28: 3 residues within 4Å: Chain B: K.218, E.219, G.220 Ligand excluded by PLIP CL.29: 3 residues within 4Å: Chain B: D.224, S.248, G.250 Ligand excluded by PLIP CL.30: 2 residues within 4Å: Chain B: I.156, P.157 Ligand excluded by PLIP CL.36: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.37: 3 residues within 4Å: Chain C: R.179, S.180, G.181 Ligand excluded by PLIP CL.47: 1 residues within 4Å: Chain D: A.213 Ligand excluded by PLIP CL.48: 3 residues within 4Å: Chain D: A.30, S.33, R.99 Ligand excluded by PLIP CL.49: 2 residues within 4Å: Chain D: Q.35, Q.41 Ligand excluded by PLIP CL.50: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.51: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.52: 1 residues within 4Å: Chain D: F.8 Ligand excluded by PLIP CL.53: 2 residues within 4Å: Chain D: V.324, S.325 Ligand excluded by PLIP CL.54: 4 residues within 4Å: Chain D: T.247, V.249, G.250, R.320 Ligand excluded by PLIP CL.55: 3 residues within 4Å: Chain C: P.57 Chain D: N.170, R.174 Ligand excluded by PLIP CL.56: 1 residues within 4Å: Chain B: R.149 Ligand excluded by PLIP CL.57: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.58: 3 residues within 4Å: Chain D: K.218, E.219, G.220 Ligand excluded by PLIP CL.59: 3 residues within 4Å: Chain D: D.224, S.248, G.250 Ligand excluded by PLIP CL.60: 2 residues within 4Å: Chain D: I.156, P.157 Ligand excluded by PLIP

2 x HVK: pyridin-2-amine(Non-covalent)

HVK.8: 5 residues within 4Å: Chain B: T.2, L.3, L.4, N.5, P.6 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:N.5 Hydrogen bonds: B:N.5 Water bridges: B:T.2, B:T.2, B:N.5 HVK.38: 5 residues within 4Å: Chain D: T.2, L.3, L.4, N.5, P.6 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:N.5 Hydrogen bonds: D:T.2, D:N.5 Water bridges: D:T.2, D:T.2, D:N.5

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)

1D0.12: 28 residues within 4Å: Chain B: A.84, H.85, K.86, E.108, T.109, G.110, A.111, G.112, A.113, H.114, L.165, C.169, G.188, T.189, C.229, V.230, G.231, G.232, G.233, S.234, N.235, G.302, L.303, F.305, A.347, E.349, S.376, G.377 30 PLIP interactions: 30 interactions with chain B Hydrophobic interactions: B:A.84, B:L.165, B:L.165, B:T.189, B:A.347, B:E.349 Hydrogen bonds: B:H.85, B:K.86, B:E.108, B:T.109, B:G.110, B:A.111, B:G.112, B:A.113, B:H.114, B:T.189, B:G.231, B:G.233, B:S.234, B:S.234, B:N.235, B:N.235, B:S.376 Water bridges: B:G.233, B:A.236 Salt bridges: B:H.85, B:K.86, B:K.86 pi-Stacking: B:H.85, B:F.305 1D0.42: 28 residues within 4Å: Chain D: A.84, H.85, K.86, E.108, T.109, G.110, A.111, G.112, A.113, H.114, L.165, C.169, G.188, T.189, C.229, V.230, G.231, G.232, G.233, S.234, N.235, G.302, L.303, F.305, A.347, E.349, S.376, G.377 29 PLIP interactions: 29 interactions with chain D Hydrophobic interactions: D:A.84, D:L.165, D:L.165, D:T.189, D:A.347, D:E.349 Hydrogen bonds: D:K.86, D:E.108, D:E.108, D:G.110, D:A.111, D:G.112, D:A.113, D:H.114, D:T.189, D:G.231, D:G.233, D:S.234, D:S.234, D:N.235, D:N.235, D:S.376 Water bridges: D:G.233, D:A.236 Salt bridges: D:H.85, D:K.86, D:K.86 pi-Stacking: D:H.85, D:F.305

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hilario, E. et al., Crystal structure of Salmonella typhimurium Tryptophan Synthase mutant beta-Q114A with 2-({[4-(trifluoromethoxy)phenyl]sulfonyl}amino)ethyl dihydrogen phosphate (F9F) at the alpha-site, Cesium ion at the metal coordination site, and [3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-ylmethyl]-serine (PLS) at the beta-site. To be Published

Release Date

2020-02-19

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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