SMTL ID : 6d0v.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.64 Å

Oligo State

hetero-2-2-mer

Ligands

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

DMS.1: 3 residues within 4Å: Chain A: S.55, F.72 Chain B: Q.293 Ligand excluded by PLIP DMS.2: 7 residues within 4Å: Chain A: M.1, R.3, V.123, D.124, H.146, N.147, I.148 Ligand excluded by PLIP 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: S.221, V.224, R.225, A.265, A.268 Ligand excluded by PLIP DMS.5: 8 residues within 4Å: Chain A: Y.115, V.128, V.131, F.139, R.140, P.150, I.151, F.152 Ligand excluded by PLIP DMS.14: 7 residues within 4Å: Chain A: S.180 Chain B: G.179, S.180, Y.181, E.182 Ligands: EDO.9, PEG.37 Ligand excluded by PLIP DMS.15: 11 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.12, CS.49, DMS.52 Ligand excluded by PLIP DMS.16: 3 residues within 4Å: Chain B: K.137, E.266, Y.298 Ligand excluded by PLIP DMS.17: 4 residues within 4Å: Chain B: Q.42, F.45, A.46, L.49 Ligand excluded by PLIP DMS.18: 9 residues within 4Å: Chain B: A.120, S.123, A.124, L.128, K.129, C.130, M.152, G.153, A.154 Ligand excluded by PLIP DMS.19: 4 residues within 4Å: Chain B: N.64, I.65, T.338, H.342 Ligand excluded by PLIP DMS.20: 1 residues within 4Å: Chain B: E.331 Ligand excluded by PLIP DMS.21: 3 residues within 4Å: Chain B: I.262, H.267, H.273 Ligand excluded by PLIP DMS.22: 1 residues within 4Å: Chain B: Y.8 Ligand excluded by PLIP DMS.23: 4 residues within 4Å: Chain B: V.146, F.147, R.150 Chain D: H.388 Ligand excluded by PLIP DMS.24: 5 residues within 4Å: Chain B: Q.36, K.37, D.38, P.39, Q.42 Ligand excluded by PLIP DMS.38: 3 residues within 4Å: Chain C: S.55, F.72 Chain D: Q.293 Ligand excluded by PLIP DMS.39: 7 residues within 4Å: Chain C: M.1, R.3, V.123, D.124, H.146, N.147, I.148 Ligand excluded by PLIP DMS.40: 3 residues within 4Å: Chain C: F.82, F.114, R.117 Ligand excluded by PLIP DMS.41: 5 residues within 4Å: Chain C: S.221, V.224, R.225, A.265, A.268 Ligand excluded by PLIP DMS.42: 8 residues within 4Å: Chain C: Y.115, V.128, V.131, F.139, R.140, P.150, I.151, F.152 Ligand excluded by PLIP DMS.51: 7 residues within 4Å: Chain C: S.180 Chain D: G.179, S.180, Y.181, E.182 Ligands: EDO.46, PEG.74 Ligand excluded by PLIP DMS.52: 11 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.12, DMS.15, CS.49 Ligand excluded by PLIP DMS.53: 3 residues within 4Å: Chain D: K.137, E.266, Y.298 Ligand excluded by PLIP DMS.54: 4 residues within 4Å: Chain D: Q.42, F.45, A.46, L.49 Ligand excluded by PLIP DMS.55: 9 residues within 4Å: Chain D: A.120, S.123, A.124, L.128, K.129, C.130, M.152, G.153, A.154 Ligand excluded by PLIP DMS.56: 4 residues within 4Å: Chain D: N.64, I.65, T.338, H.342 Ligand excluded by PLIP DMS.57: 1 residues within 4Å: Chain D: E.331 Ligand excluded by PLIP DMS.58: 3 residues within 4Å: Chain D: I.262, H.267, H.273 Ligand excluded by PLIP DMS.59: 1 residues within 4Å: Chain D: Y.8 Ligand excluded by PLIP DMS.60: 4 residues within 4Å: Chain B: H.388 Chain D: V.146, F.147, R.150 Ligand excluded by PLIP DMS.61: 5 residues within 4Å: Chain D: Q.36, K.37, D.38, P.39, Q.42 Ligand excluded by PLIP

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

CL.6: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain A: A.167, G.170, H.204, A.206 Ligand excluded by PLIP CL.25: 1 residues within 4Å: Chain B: Q.36 Ligand excluded by PLIP CL.26: 2 residues within 4Å: Chain B: G.153, E.155 Ligand excluded by PLIP CL.27: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.43: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.44: 4 residues within 4Å: Chain C: A.167, G.170, H.204, A.206 Ligand excluded by PLIP CL.62: 1 residues within 4Å: Chain D: Q.36 Ligand excluded by PLIP CL.63: 2 residues within 4Å: Chain D: G.153, E.155 Ligand excluded by PLIP CL.64: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

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

F9F.8: 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.18 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.100, A:L.100, A:L.127, A:Y.175, A:T.183 Hydrogen bonds: A:R.179, A:G.184, A:F.212, A:G.213, A:G.234, A:S.235 Water bridges: A:I.214, A:I.214, A:A.236 pi-Stacking: A:F.212 F9F.45: 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.18 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:L.100, C:L.100, C:L.127, C:Y.175, C:T.183 Hydrogen bonds: C:Y.175, C:R.179, C:G.184, C:F.212, C:G.213, C:G.234, C:S.235 Water bridges: C:I.214, C:I.214, C:A.236 pi-Stacking: C:F.212

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

EDO.9: 6 residues within 4Å: Chain A: R.179, S.180, G.181, N.187 Chain B: G.179 Ligands: DMS.14 Ligand excluded by PLIP EDO.28: 3 residues within 4Å: Chain B: G.265, E.295, E.296 Ligand excluded by PLIP EDO.29: 4 residues within 4Å: Chain B: E.210, E.211, A.214, Q.215 Ligand excluded by PLIP EDO.30: 4 residues within 4Å: Chain B: Y.133, E.172, R.175, D.176 Ligand excluded by PLIP EDO.31: 2 residues within 4Å: Chain B: R.363, E.364 Ligand excluded by PLIP EDO.32: 3 residues within 4Å: Chain B: Y.8, F.9, Y.315 Ligand excluded by PLIP EDO.33: 5 residues within 4Å: Chain B: P.158, V.159, H.160, S.161, E.172 Ligand excluded by PLIP EDO.34: 6 residues within 4Å: Chain B: H.273, G.274, R.275, M.286, M.287, Q.288 Ligand excluded by PLIP EDO.46: 6 residues within 4Å: Chain C: R.179, S.180, G.181, N.187 Chain D: G.179 Ligands: DMS.51 Ligand excluded by PLIP EDO.65: 3 residues within 4Å: Chain D: G.265, E.295, E.296 Ligand excluded by PLIP EDO.66: 4 residues within 4Å: Chain D: E.210, E.211, A.214, Q.215 Ligand excluded by PLIP EDO.67: 4 residues within 4Å: Chain D: Y.133, E.172, R.175, D.176 Ligand excluded by PLIP EDO.68: 2 residues within 4Å: Chain D: R.363, E.364 Ligand excluded by PLIP EDO.69: 3 residues within 4Å: Chain D: Y.8, F.9, Y.315 Ligand excluded by PLIP EDO.70: 5 residues within 4Å: Chain D: P.158, V.159, H.160, S.161, E.172 Ligand excluded by PLIP EDO.71: 6 residues within 4Å: Chain D: H.273, G.274, R.275, M.286, M.287, Q.288 Ligand excluded by PLIP

2 x 0JO: 2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid(Non-covalent)

0JO.10: 24 residues within 4Å: Chain B: A.85, H.86, K.87, T.110, G.111, A.112, G.113, A.114, H.115, L.166, T.190, C.230, V.231, G.232, G.233, G.234, S.235, N.236, G.303, L.304, A.348, E.350, S.377, G.378 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:A.85, B:L.166, B:A.348, B:E.350 Hydrogen bonds: B:K.87, B:G.111, B:A.112, B:G.113, B:A.114, B:H.115, B:T.190, B:T.190, B:G.232, B:G.234, B:S.235, B:N.236, B:N.236, B:S.377 Water bridges: B:E.109, B:G.233, B:G.233, B:A.237 Salt bridges: B:H.86, B:K.87, B:K.87 pi-Stacking: B:H.86 0JO.47: 24 residues within 4Å: Chain D: A.85, H.86, K.87, T.110, G.111, A.112, G.113, A.114, H.115, L.166, T.190, C.230, V.231, G.232, G.233, G.234, S.235, N.236, G.303, L.304, A.348, E.350, S.377, G.378 26 PLIP interactions: 26 interactions with chain D Hydrophobic interactions: D:A.85, D:L.166, D:A.348, D:E.350 Hydrogen bonds: D:K.87, D:T.110, D:G.111, D:A.112, D:G.113, D:A.114, D:H.115, D:T.190, D:G.232, D:G.234, D:S.235, D:N.236, D:N.236, D:S.377 Water bridges: D:E.109, D:G.233, D:G.233, D:A.237 Salt bridges: D:H.86, D:K.87, D:K.87 pi-Stacking: D:H.86

6 x CS: CESIUM ION(Non-covalent)

CS.11: 6 residues within 4Å: Chain B: V.231, G.232, G.268, L.304, F.306, S.308 No protein-ligand interaction detected (PLIP) CS.12: 7 residues within 4Å: Chain B: G.54, P.56 Chain D: G.54, P.56 Ligands: DMS.15, CS.49, DMS.52 No protein-ligand interaction detected (PLIP) CS.13: 3 residues within 4Å: Chain B: T.66, T.69, T.71 No protein-ligand interaction detected (PLIP) CS.48: 6 residues within 4Å: Chain D: V.231, G.232, G.268, L.304, F.306, S.308 No protein-ligand interaction detected (PLIP) CS.49: 7 residues within 4Å: Chain B: G.54, P.56 Chain D: G.54, P.56 Ligands: CS.12, DMS.15, DMS.52 No protein-ligand interaction detected (PLIP) CS.50: 3 residues within 4Å: Chain D: T.66, T.69, T.71 No protein-ligand interaction detected (PLIP)

2 x SER: SERINE(Non-covalent)

SER.35: 9 residues within 4Å: Chain A: S.55, D.56, P.57, Q.65, L.69 Chain B: S.161, G.162, N.171, R.175 9 PLIP interactions: 7 interactions with chain B, 1 Ligand-Ligand interactions, 1 interactions with chain A Hydrogen bonds: B:G.162, B:N.171, A:D.56 Water bridges: B:S.161, B:S.161, B:K.167, B:D.168, S.35 Salt bridges: B:R.175 SER.72: 9 residues within 4Å: Chain C: S.55, D.56, P.57, Q.65, L.69 Chain D: S.161, G.162, N.171, R.175 10 PLIP interactions: 2 interactions with chain C, 7 interactions with chain D, 1 Ligand-Ligand interactions Hydrogen bonds: C:D.56, C:D.56, D:G.162, D:N.171 Water bridges: D:S.161, D:S.161, D:E.296, D:E.296, S.72 Salt bridges: D:R.175

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

PEG.36: 6 residues within 4Å: Chain B: T.60, K.61, E.343 Chain D: N.51, Y.52, L.125 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain B Water bridges: D:N.51, D:N.51, B:L.59 Hydrogen bonds: B:K.61, B:E.343 PEG.37: 5 residues within 4Å: Chain B: G.179, S.180, E.182, T.183 Ligands: DMS.14 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.182, B:T.183, B:T.183 PEG.73: 6 residues within 4Å: Chain B: N.51, Y.52, L.125 Chain D: T.60, K.61, E.343 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:K.61, D:E.343, D:E.343 Water bridges: D:L.59, B:N.51, B:N.51 PEG.74: 5 residues within 4Å: Chain D: G.179, S.180, E.182, T.183 Ligands: DMS.51 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.182, D:T.183 Water bridges: D:T.183

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hilario, E. et al., Tryptophan synthase Q114A mutant in complex with inhibitor N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the alpha-site, aminoacrylate at the beta site, and cesium ion at the metal coordination site. To be Published

Release Date

2019-04-17

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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