SMTL ID : 3cep.1

Structure of a tryptophan synthase quinonoid intermediate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-2-2-mer

Ligands

2 x G3P: SN-GLYCEROL-3-PHOSPHATE(Non-covalent)

G3P.1: 11 residues within 4Å: Chain A: E.49, I.64, Y.175, T.183, G.184, F.212, G.213, I.232, G.234, S.235 Ligands: IDM.2 9 PLIP interactions: 9 interactions with chain A 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 G3P.9: 11 residues within 4Å: Chain C: E.49, I.64, Y.175, T.183, G.184, F.212, G.213, I.232, G.234, S.235 Ligands: IDM.10 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:Y.175, C:Y.175, 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

4 x IDM: INDOLINE(Non-covalent)

IDM.2: 12 residues within 4Å: Chain A: F.22, E.49, A.59, D.60, I.64, L.100, L.127, A.129, Y.175, T.183, F.212 Ligands: G3P.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:A.59, A:I.64, A:L.100, A:L.100, A:L.100, A:L.127, A:A.129, A:Y.175, A:T.183 pi-Stacking: A:F.22, A:F.212 IDM.8: 12 residues within 4Å: Chain B: K.86, E.108, H.114, L.165, G.188, T.189, G.231, G.232, G.302, F.305 Ligands: PLP.6, MH6.7 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:E.108, B:L.165, B:L.165, B:T.189 Hydrogen bonds: B:K.86 pi-Stacking: B:F.305 IDM.10: 12 residues within 4Å: Chain C: F.22, E.49, A.59, D.60, I.64, L.100, L.127, A.129, Y.175, T.183, F.212 Ligands: G3P.9 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:A.59, C:I.64, C:L.100, C:L.100, C:L.100, C:L.127, C:A.129, C:Y.175, C:T.183 pi-Stacking: C:F.22, C:F.212 IDM.16: 12 residues within 4Å: Chain D: K.86, E.108, H.114, L.165, G.188, T.189, G.231, G.232, G.302, F.305 Ligands: PLP.14, MH6.15 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:E.108, D:L.165, D:L.165, D:T.189 Hydrogen bonds: D:K.86 pi-Stacking: D:F.305

6 x CS: CESIUM ION(Non-covalent)

CS.3: 6 residues within 4Å: Chain B: V.230, G.231, G.267, L.303, F.305, S.307 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:G.231, B:F.305, H2O.10 CS.4: 5 residues within 4Å: Chain B: G.53, P.55 Chain D: G.53, P.55 Ligands: CS.12 No protein-ligand interaction detected (PLIP) CS.5: 3 residues within 4Å: Chain B: T.65, T.68, T.70 No protein-ligand interaction detected (PLIP) CS.11: 6 residues within 4Å: Chain D: V.230, G.231, G.267, L.303, F.305, S.307 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:G.231, D:F.305, H2O.21 CS.12: 5 residues within 4Å: Chain B: G.53, P.55 Chain D: G.53, P.55 Ligands: CS.4 No protein-ligand interaction detected (PLIP) CS.13: 3 residues within 4Å: Chain D: T.65, T.68, T.70 No protein-ligand interaction detected (PLIP)

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Non-covalent)

PLP.6: 21 residues within 4Å: Chain B: A.84, H.85, K.86, A.111, Q.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 Ligands: MH6.7, IDM.8 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:A.84, B:A.347, B:E.349 Hydrogen bonds: B:T.189, 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:A.236 Salt bridges: B:H.85, B:K.86 pi-Stacking: B:H.85 PLP.14: 21 residues within 4Å: Chain D: A.84, H.85, K.86, A.111, Q.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 Ligands: MH6.15, IDM.16 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:A.84, D:A.347, D:E.349 Hydrogen bonds: 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:A.236 Salt bridges: D:H.85, D:K.86 pi-Stacking: D:H.85

2 x MH6: 3-hydroxy-2-iminopropanoic acid(Non-covalent)

MH6.7: 11 residues within 4Å: Chain B: K.86, T.109, G.110, A.111, G.112, Q.113, H.114, L.165, G.302 Ligands: PLP.6, IDM.8 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.165 Hydrogen bonds: B:K.86, B:G.110, B:A.111, B:G.112, B:Q.113, B:H.114 Salt bridges: B:K.86 MH6.15: 11 residues within 4Å: Chain D: K.86, T.109, G.110, A.111, G.112, Q.113, H.114, L.165, G.302 Ligands: PLP.14, IDM.16 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:L.165 Hydrogen bonds: D:K.86, D:T.109, D:G.110, D:A.111, D:G.112, D:Q.113, D:H.114 Salt bridges: D:K.86

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Barends, T.R. et al., Structure and mechanistic implications of a tryptophan synthase quinonoid intermediate. Chembiochem (2008)

Release Date

2008-04-01

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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