SMTL ID : 6c73.1

Tryptophan synthase Q114A mutant (internal aldimine state) in complex with N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) with cesium ion bound in the metal coordination site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

hetero-2-2-mer

Ligands

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

DMS.1: 5 residues within 4Å: Chain A: I.41, H.92, P.93, T.94, I.95 Ligand excluded by PLIP DMS.2: 8 residues within 4Å: Chain A: V.128, V.131, S.136, F.139, R.140, P.150, I.151, F.152 Ligand excluded by PLIP DMS.3: 4 residues within 4Å: Chain A: S.55, L.69, F.72 Chain B: G.161 Ligand excluded by PLIP DMS.4: 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.5: 7 residues within 4Å: Chain A: L.191, P.192, L.193, H.194, Q.210, A.222, A.226 Ligand excluded by PLIP DMS.6: 3 residues within 4Å: Chain A: F.82, F.114, R.117 Ligand excluded by PLIP DMS.7: 4 residues within 4Å: Chain A: L.34, K.35, D.38, K.91 Ligand excluded by PLIP DMS.8: 6 residues within 4Å: Chain A: L.11, N.12, R.15, E.16, G.17, V.224 Ligand excluded by PLIP DMS.9: 2 residues within 4Å: Chain A: R.267, A.268 Ligand excluded by PLIP DMS.15: 4 residues within 4Å: Chain B: Y.132, E.171, R.174, D.175 Ligand excluded by PLIP DMS.16: 9 residues within 4Å: Chain B: K.49, G.53, R.54, P.55 Chain D: P.55, T.56, A.57, Q.214 Ligands: DMS.49 Ligand excluded by PLIP DMS.17: 5 residues within 4Å: Chain B: Q.41, F.44, A.45, L.48, M.206 Ligand excluded by PLIP DMS.18: 2 residues within 4Å: Chain B: L.270, N.316 Ligand excluded by PLIP DMS.19: 2 residues within 4Å: Chain B: K.98, R.99 Ligand excluded by PLIP DMS.20: 5 residues within 4Å: Chain B: I.261, G.264, H.266, H.272 Ligands: DMS.22 Ligand excluded by PLIP DMS.21: 4 residues within 4Å: Chain B: T.2, L.3, L.4, N.5 Ligand excluded by PLIP DMS.22: 6 residues within 4Å: Chain B: H.272, G.273, M.286, Q.287, E.294 Ligands: DMS.20 Ligand excluded by PLIP DMS.23: 6 residues within 4Å: Chain B: Q.35, K.36, D.37, P.38, Q.41 Ligands: EDO.29 Ligand excluded by PLIP DMS.24: 3 residues within 4Å: Chain B: R.149, L.150 Chain D: L.390 Ligand excluded by PLIP DMS.25: 5 residues within 4Å: Chain B: S.142, P.143 Chain D: I.383, F.384, H.387 Ligand excluded by PLIP DMS.34: 5 residues within 4Å: Chain C: I.41, H.92, P.93, T.94, I.95 Ligand excluded by PLIP DMS.35: 8 residues within 4Å: Chain C: V.128, V.131, S.136, F.139, R.140, P.150, I.151, F.152 Ligand excluded by PLIP DMS.36: 4 residues within 4Å: Chain C: S.55, L.69, F.72 Chain D: G.161 Ligand excluded by PLIP DMS.37: 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.38: 7 residues within 4Å: Chain C: L.191, P.192, L.193, H.194, Q.210, A.222, A.226 Ligand excluded by PLIP DMS.39: 3 residues within 4Å: Chain C: F.82, F.114, R.117 Ligand excluded by PLIP DMS.40: 4 residues within 4Å: Chain C: L.34, K.35, D.38, K.91 Ligand excluded by PLIP DMS.41: 6 residues within 4Å: Chain C: L.11, N.12, R.15, E.16, G.17, V.224 Ligand excluded by PLIP DMS.42: 2 residues within 4Å: Chain C: R.267, A.268 Ligand excluded by PLIP DMS.48: 4 residues within 4Å: Chain D: Y.132, E.171, R.174, D.175 Ligand excluded by PLIP DMS.49: 9 residues within 4Å: Chain B: P.55, T.56, A.57, Q.214 Chain D: K.49, G.53, R.54, P.55 Ligands: DMS.16 Ligand excluded by PLIP DMS.50: 5 residues within 4Å: Chain D: Q.41, F.44, A.45, L.48, M.206 Ligand excluded by PLIP DMS.51: 2 residues within 4Å: Chain D: L.270, N.316 Ligand excluded by PLIP DMS.52: 2 residues within 4Å: Chain D: K.98, R.99 Ligand excluded by PLIP DMS.53: 5 residues within 4Å: Chain D: I.261, G.264, H.266, H.272 Ligands: DMS.55 Ligand excluded by PLIP DMS.54: 4 residues within 4Å: Chain D: T.2, L.3, L.4, N.5 Ligand excluded by PLIP DMS.55: 6 residues within 4Å: Chain D: H.272, G.273, M.286, Q.287, E.294 Ligands: DMS.53 Ligand excluded by PLIP DMS.56: 6 residues within 4Å: Chain D: Q.35, K.36, D.37, P.38, Q.41 Ligands: EDO.62 Ligand excluded by PLIP DMS.57: 3 residues within 4Å: Chain B: L.390 Chain D: R.149, L.150 Ligand excluded by PLIP DMS.58: 5 residues within 4Å: Chain B: I.383, F.384, H.387 Chain D: S.142, P.143 Ligand excluded by PLIP

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

F9F.10: 19 residues within 4Å: Chain A: F.22, E.49, A.59, I.64, L.100, L.127, A.129, I.153, Y.175, L.177, 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:I.153, A:Y.175, A:T.183 Hydrogen bonds: A:Y.175, 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.43: 19 residues within 4Å: Chain C: F.22, E.49, A.59, I.64, L.100, L.127, A.129, I.153, Y.175, L.177, 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:I.153, C:Y.175, C:T.183 Hydrogen bonds: 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

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

PEG.11: 9 residues within 4Å: Chain A: F.107, I.111, E.135, P.138, F.139 Chain B: Y.7, Y.15, I.277, K.282 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.15, B:K.282, A:E.135 Water bridges: B:Y.7, B:Y.7 PEG.44: 9 residues within 4Å: Chain C: F.107, I.111, E.135, P.138, F.139 Chain D: Y.7, Y.15, I.277, K.282 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:Y.7, D:K.282, C:E.135, C:E.135 Water bridges: D:Y.15, D:Y.15

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

EDO.12: 4 residues within 4Å: Chain A: P.217, S.257, F.258, A.261 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.257 EDO.26: 5 residues within 4Å: Chain A: F.107 Chain B: E.10, F.11, V.275, K.282 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.282, B:K.282 EDO.27: 5 residues within 4Å: Chain B: I.64, T.337, H.341, M.361, R.362 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.341, B:R.362, B:R.362 EDO.28: 4 residues within 4Å: Chain B: R.69, E.366, K.367, E.368 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.368, B:E.368 Water bridges: B:R.69, B:E.366 EDO.29: 3 residues within 4Å: Chain B: Q.35, Q.41 Ligands: DMS.23 2 PLIP interactions: 2 interactions with chain B Water bridges: B:Q.35, B:Q.41 EDO.45: 4 residues within 4Å: Chain C: P.217, S.257, F.258, A.261 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.257 EDO.59: 5 residues within 4Å: Chain C: F.107 Chain D: E.10, F.11, V.275, K.282 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.282, D:K.282 EDO.60: 5 residues within 4Å: Chain D: I.64, T.337, H.341, M.361, R.362 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:H.341, D:R.362, D:R.362 EDO.61: 4 residues within 4Å: Chain D: R.69, E.366, K.367, E.368 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:E.368, D:E.368 Water bridges: D:R.69, D:E.366 EDO.62: 3 residues within 4Å: Chain D: Q.35, Q.41 Ligands: DMS.56 2 PLIP interactions: 2 interactions with chain D Water bridges: D:Q.35, D:Q.41

8 x CS: CESIUM ION(Non-covalent)

CS.13: 3 residues within 4Å: Chain A: A.167, G.170, H.204 No protein-ligand interaction detected (PLIP) CS.30: 7 residues within 4Å: Chain B: V.230, G.231, G.267, S.296, L.303, F.305, S.307 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:G.267 CS.31: 3 residues within 4Å: Chain B: T.65, T.68, T.70 No protein-ligand interaction detected (PLIP) CS.32: 1 residues within 4Å: Chain B: E.10 No protein-ligand interaction detected (PLIP) CS.46: 3 residues within 4Å: Chain C: A.167, G.170, H.204 No protein-ligand interaction detected (PLIP) CS.63: 7 residues within 4Å: Chain D: V.230, G.231, G.267, S.296, L.303, F.305, S.307 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:G.267 CS.64: 3 residues within 4Å: Chain D: T.65, T.68, T.70 No protein-ligand interaction detected (PLIP) CS.65: 1 residues within 4Å: Chain D: E.10 No protein-ligand interaction detected (PLIP)

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)

PLP.14: 18 residues within 4Å: Chain B: A.84, H.85, K.86, A.113, T.189, C.229, V.230, G.231, G.232, G.233, S.234, N.235, G.302, L.303, A.347, E.349, S.376, G.377 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:A.84, B:K.86, B:A.347 Hydrogen bonds: B:T.189, B:G.231, B:G.232, B:G.233, B:S.234, B:N.235, B:N.235, B:S.376 Water bridges: B:T.189, B:T.189, B:S.234, B:S.234, B:A.236 Salt bridges: B:H.85, B:K.86 pi-Stacking: B:H.85 PLP.47: 18 residues within 4Å: Chain D: A.84, H.85, K.86, A.113, T.189, C.229, V.230, G.231, G.232, G.233, S.234, N.235, G.302, L.303, A.347, E.349, S.376, G.377 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:A.84, D:K.86, D:A.347 Hydrogen bonds: D:T.189, D:T.189, D:G.231, D:G.232, D:G.233, D:S.234, D:N.235, D:N.235, D:S.376 Water bridges: D:S.234, D:S.234, D:A.236 Salt bridges: D:H.85, D:K.86 pi-Stacking: D:H.85

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

CL.33: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.66: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hilario, E. et al., Tryptophan synthase Q114A mutant (internal aldimine state) in complex with N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) with cesium ion bound in the metal coordination site. To be Published

Release Date

2019-01-23

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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