SMTL ID : 4hpx.2 (1 other biounit)

Crystal structure of Tryptophan Synthase at 1.65 A resolution in complex with alpha aminoacrylate E(A-A) and benzimidazole in the beta site and the F9 inhibitor in the alpha site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 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 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: 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 pi-Stacking: A:F.212 F9F.16: 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 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: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 pi-Stacking: C:F.212

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

PEG.2: 4 residues within 4Å: Chain A: R.164, Q.165, S.168, Y.169 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.168 PEG.10: 4 residues within 4Å: Chain B: E.263, T.264 Ligands: BCN.8, PEG.11 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.263 PEG.11: 5 residues within 4Å: Chain B: I.262, E.263, T.264, G.265 Ligands: PEG.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.262 PEG.12: 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:A.214, B:D.218 PEG.13: 7 residues within 4Å: Chain A: S.180 Chain B: E.105, G.179, S.180, Y.181, E.182, T.183 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.180, B:E.182, B:T.183 PEG.17: 4 residues within 4Å: Chain C: R.164, Q.165, S.168, Y.169 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.168 PEG.25: 4 residues within 4Å: Chain D: E.263, T.264 Ligands: BCN.23, PEG.26 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.263, D:E.263 PEG.26: 5 residues within 4Å: Chain D: I.262, E.263, T.264, G.265 Ligands: PEG.25 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:I.262 PEG.27: 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:A.214, D:D.218 PEG.28: 7 residues within 4Å: Chain C: S.180 Chain D: E.105, G.179, S.180, Y.181, E.182, T.183 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:E.182, D:T.183, C:S.180

6 x BZI: BENZIMIDAZOLE(Non-covalent)

BZI.3: 10 residues within 4Å: Chain B: K.87, E.109, L.166, C.170, G.189, T.190, G.232, G.233, F.306 Ligands: 0JO.6 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.166, B:L.166, B:T.190, B:F.306 Hydrogen bonds: B:K.87, B:K.87, B:E.109, B:G.189 pi-Stacking: B:F.306 BZI.4: 4 residues within 4Å: Chain B: T.3, L.4, L.5, N.6 No protein-ligand interaction detected (PLIP) BZI.5: 2 residues within 4Å: Chain B: A.136, K.137 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:K.137, B:K.137 BZI.18: 10 residues within 4Å: Chain D: K.87, E.109, L.166, C.170, G.189, T.190, G.232, G.233, F.306 Ligands: 0JO.21 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:L.166, D:L.166, D:T.190, D:F.306 Hydrogen bonds: D:K.87, D:K.87, D:G.189 pi-Stacking: D:F.306 BZI.19: 4 residues within 4Å: Chain D: T.3, L.4, L.5, N.6 No protein-ligand interaction detected (PLIP) BZI.20: 2 residues within 4Å: Chain D: A.136, K.137 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:K.137, D:K.137

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

0JO.6: 25 residues within 4Å: Chain B: A.85, H.86, K.87, T.110, G.111, A.112, G.113, Q.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 Ligands: BZI.3 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:A.85, B:L.166, B:A.348, B:E.350 Hydrogen bonds: B:G.111, B:A.112, B:G.113, B:Q.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:A.237 Salt bridges: B:H.86, B:K.87, B:K.87 pi-Stacking: B:H.86 0JO.21: 25 residues within 4Å: Chain D: A.85, H.86, K.87, T.110, G.111, A.112, G.113, Q.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 Ligands: BZI.18 23 PLIP interactions: 23 interactions with chain D Hydrophobic interactions: D:A.85, D:L.166, D:A.348, D:E.350 Hydrogen bonds: D:T.110, D:G.111, D:A.112, D:G.113, D:Q.114, D:H.115, 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:A.237 Salt bridges: D:H.86, D:K.87, D:K.87 pi-Stacking: D:H.86

6 x BCN: BICINE(Non-covalent)

BCN.7: 9 residues within 4Å: Chain B: T.248, S.249, V.250, G.251, L.252, G.320, R.321, A.322, D.323 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.249, B:L.252, B:L.252, B:R.321 Salt bridges: B:R.321, B:D.323 BCN.8: 7 residues within 4Å: Chain B: G.259, H.260, E.263, T.328, D.329, D.330 Ligands: PEG.10 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.263, B:D.330, B:D.330 Salt bridges: B:D.330 BCN.9: 5 residues within 4Å: Chain A: T.77 Chain B: T.289, A.290, D.291, Q.293 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.289, B:D.291 Water bridges: B:A.290, B:A.290 Salt bridges: B:D.291 BCN.22: 9 residues within 4Å: Chain D: T.248, S.249, V.250, G.251, L.252, G.320, R.321, A.322, D.323 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:S.249, D:L.252, D:L.252, D:R.321 Salt bridges: D:R.321, D:D.323 BCN.23: 7 residues within 4Å: Chain D: G.259, H.260, E.263, T.328, D.329, D.330 Ligands: PEG.25 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:E.263, D:T.328, D:D.330 Water bridges: D:D.329 Salt bridges: D:D.330 BCN.24: 5 residues within 4Å: Chain C: T.77 Chain D: T.289, A.290, D.291, Q.293 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:T.289, D:D.291, D:D.291 Water bridges: D:A.290, D:A.290 Salt bridges: D:D.291

4 x CS: CESIUM ION(Non-covalent)

CS.14: 6 residues within 4Å: Chain B: V.231, G.232, G.268, L.304, F.306, S.308 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:G.232, B:F.306, H2O.28 CS.15: 3 residues within 4Å: Chain B: T.66, T.69, T.71 No protein-ligand interaction detected (PLIP) CS.29: 6 residues within 4Å: Chain D: V.231, G.232, G.268, L.304, F.306, S.308 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:G.232, D:F.306, H2O.56 CS.30: 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

2013-12-18

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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