SMTL ID : 4hpj.1

Crystal structure of Tryptophan Synthase at 1.45 A resolution in complex with 2-aminophenol quinonoid in the beta site and the F9 inhibitor in the alpha site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

hetero-2-2-mer

Ligands

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

F9F.1: 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 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.100, 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:I.214, A:I.214, A:A.236 pi-Stacking: A:F.212 F9F.17: 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 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:L.100, 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:I.214, C:I.214, C:A.236 pi-Stacking: C:F.212

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

CL.2: 1 residues within 4Å: Chain A: P.138 Ligand excluded by PLIP CL.9: 1 residues within 4Å: Chain B: N.6 Ligand excluded by PLIP CL.10: 1 residues within 4Å: Chain B: F.9 Ligand excluded by PLIP CL.11: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.12: 1 residues within 4Å: Chain B: N.6 Ligand excluded by PLIP CL.13: 4 residues within 4Å: Chain A: N.157 Chain B: I.20, P.23, Y.181 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain B: H.260, E.263 Ligand excluded by PLIP CL.18: 1 residues within 4Å: Chain C: P.138 Ligand excluded by PLIP CL.25: 1 residues within 4Å: Chain D: N.6 Ligand excluded by PLIP CL.26: 1 residues within 4Å: Chain D: F.9 Ligand excluded by PLIP CL.27: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.28: 1 residues within 4Å: Chain D: N.6 Ligand excluded by PLIP CL.29: 4 residues within 4Å: Chain C: N.157 Chain D: I.20, P.23, Y.181 Ligand excluded by PLIP CL.30: 2 residues within 4Å: Chain D: H.260, E.263 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)

1D0.3: 27 residues within 4Å: Chain B: A.85, H.86, K.87, E.109, T.110, G.111, A.112, G.113, Q.114, H.115, L.166, G.189, T.190, C.230, V.231, G.232, G.233, G.234, S.235, N.236, G.303, L.304, F.306, A.348, E.350, S.377, G.378 30 PLIP interactions: 30 interactions with chain B Hydrophobic interactions: B:A.85, B:L.166, B:T.190, B:A.348, B:E.350 Hydrogen bonds: B:K.87, B:K.87, B:E.109, B:T.110, B:G.111, B:A.112, B:G.113, B:Q.114, B:H.115, B:G.189, B:T.190, B:G.232, 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 1D0.19: 27 residues within 4Å: Chain D: A.85, H.86, K.87, E.109, T.110, G.111, A.112, G.113, Q.114, H.115, L.166, G.189, T.190, C.230, V.231, G.232, G.233, G.234, S.235, N.236, G.303, L.304, F.306, A.348, E.350, S.377, G.378 31 PLIP interactions: 31 interactions with chain D Hydrophobic interactions: D:A.85, D:L.166, D:T.190, D:A.348, D:E.350 Hydrogen bonds: D:K.87, D:K.87, D:E.109, D:E.109, D:G.111, D:A.112, D:G.113, D:Q.114, D:H.115, D:G.189, 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

2 x BCN: BICINE(Non-covalent)

BCN.4: 9 residues within 4Å: Chain B: T.248, S.249, V.250, G.251, L.252, G.320, R.321, A.322, D.323 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.249, B:L.252, B:L.252, B:R.321, B:R.321 Salt bridges: B:R.321, B:D.323 BCN.20: 9 residues within 4Å: Chain D: T.248, S.249, V.250, G.251, L.252, G.320, R.321, A.322, D.323 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:S.249, D:L.252, D:L.252, D:R.321, D:R.321 Salt bridges: D:R.321, D:D.323

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

PEG.5: 4 residues within 4Å: Chain B: T.3, L.4, L.5, N.6 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.4 Water bridges: B:N.6 PEG.6: 4 residues within 4Å: Chain B: T.328, D.330, E.331, E.334 1 PLIP interactions: 1 interactions with chain B Water bridges: B:T.328 PEG.7: 5 residues within 4Å: Chain B: P.56, E.211, A.214, Q.215, D.218 2 PLIP interactions: 2 interactions with chain B Water bridges: B:E.210, B:D.218 PEG.8: 5 residues within 4Å: Chain B: L.217, D.218, K.219, E.220, G.221 No protein-ligand interaction detected (PLIP) PEG.21: 4 residues within 4Å: Chain D: T.3, L.4, L.5, N.6 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:L.4 Water bridges: D:N.6 PEG.22: 4 residues within 4Å: Chain D: T.328, D.330, E.331, E.334 2 PLIP interactions: 2 interactions with chain D Water bridges: D:T.328, D:E.331 PEG.23: 5 residues within 4Å: Chain D: P.56, E.211, A.214, Q.215, D.218 2 PLIP interactions: 2 interactions with chain D Water bridges: D:E.210, D:D.218 PEG.24: 5 residues within 4Å: Chain D: L.217, D.218, K.219, E.220, G.221 No protein-ligand interaction detected (PLIP)

4 x CS: CESIUM ION(Non-covalent)

CS.15: 6 residues within 4Å: Chain B: V.231, G.232, G.268, L.304, F.306, S.308 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:G.232 CS.16: 3 residues within 4Å: Chain B: T.66, T.69, T.71 No protein-ligand interaction detected (PLIP) CS.31: 6 residues within 4Å: Chain D: V.231, G.232, G.268, L.304, F.306, S.308 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:G.232 CS.32: 3 residues within 4Å: Chain D: T.66, T.69, T.71 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Niks, D. et al., Allostery and substrate channeling in the tryptophan synthase bienzyme complex: evidence for two subunit conformations and four quaternary states. Biochemistry (2013)

Release Date

2013-12-25

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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