SMTL ID : 2fwn.1

Phosphorylation of an active site serine in a ThDP-dependent enzyme by phosphonate inactivation

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 7 residues within 4Å: Chain A: N.117, L.118, R.120 Chain B: N.117, L.118, R.120 Ligands: MG.6 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Metal complexes: A:N.117, A:L.118, A:R.120, B:N.117, B:L.118, B:R.120 MG.6: 7 residues within 4Å: Chain A: N.117, L.118, R.120 Chain B: N.117, L.118, R.120 Ligands: MG.1 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Metal complexes: A:N.117, A:L.118, A:R.120, B:N.117, B:L.118, B:R.120 MG.11: 7 residues within 4Å: Chain C: N.117, L.118, R.120 Chain D: N.117, L.118, R.120 Ligands: MG.16 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain C Metal complexes: D:N.117, D:L.118, D:R.120, C:N.117, C:L.118, C:R.120 MG.16: 7 residues within 4Å: Chain C: N.117, L.118, R.120 Chain D: N.117, L.118, R.120 Ligands: MG.11 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain C Metal complexes: D:N.117, D:L.118, D:R.120, C:N.117, C:L.118, C:R.120

12 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: D.428, N.455, T.457 Ligands: TPP.5 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.428, A:T.457, H2O.22 CA.3: 1 residues within 4Å: Chain A: D.364 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.364, H2O.11, H2O.17, H2O.23, H2O.27 CA.4: 1 residues within 4Å: Chain A: A.416 5 PLIP interactions: 5 Ligand-Water interactions Metal complexes: H2O.8, H2O.23, H2O.27, H2O.27, H2O.27 CA.7: 4 residues within 4Å: Chain B: D.428, N.455, T.457 Ligands: TPP.10 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.428, B:T.457, H2O.49 CA.8: 1 residues within 4Å: Chain B: D.364 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.364, H2O.38, H2O.44, H2O.50, H2O.55 CA.9: 1 residues within 4Å: Chain B: A.416 5 PLIP interactions: 5 Ligand-Water interactions Metal complexes: H2O.35, H2O.50, H2O.54, H2O.54, H2O.54 CA.12: 4 residues within 4Å: Chain C: D.428, N.455, T.457 Ligands: TPP.15 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.428, C:T.457, H2O.77 CA.13: 1 residues within 4Å: Chain C: D.364 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:D.364, H2O.66, H2O.72, H2O.77, H2O.82 CA.14: 1 residues within 4Å: Chain C: A.416 5 PLIP interactions: 5 Ligand-Water interactions Metal complexes: H2O.63, H2O.77, H2O.82, H2O.82, H2O.82 CA.17: 4 residues within 4Å: Chain D: D.428, N.455, T.457 Ligands: TPP.20 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.428, D:T.457, H2O.104 CA.18: 1 residues within 4Å: Chain D: D.364 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:D.364, H2O.93, H2O.99, H2O.105, H2O.109 CA.19: 1 residues within 4Å: Chain D: A.416 5 PLIP interactions: 5 Ligand-Water interactions Metal complexes: H2O.90, H2O.104, H2O.109, H2O.109, H2O.109

4 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.5: 26 residues within 4Å: Chain A: E.375, S.376, T.377, S.378, G.401, G.402, L.403, G.427, D.428, G.429, S.430, Y.433, N.455, T.457, Y.458, G.459, A.460, L.461 Chain B: N.23, P.24, G.25, S.26, E.47, H.70, N.77 Ligands: CA.2 18 PLIP interactions: 17 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.403, A:Y.433, A:L.461 Hydrogen bonds: A:S.376, A:T.377, A:S.378, A:G.401, A:L.403, A:G.429, A:S.430, A:Y.433, A:N.455, A:G.459, A:A.460 Water bridges: A:S.378, A:D.428, A:N.455, B:H.70 TPP.10: 26 residues within 4Å: Chain A: N.23, P.24, G.25, S.26, E.47, H.70, N.77 Chain B: E.375, S.376, T.377, S.378, G.401, G.402, L.403, G.427, D.428, G.429, S.430, Y.433, N.455, T.457, Y.458, G.459, A.460, L.461 Ligands: CA.7 18 PLIP interactions: 17 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.403, B:Y.433, B:L.461 Hydrogen bonds: B:S.376, B:T.377, B:S.378, B:G.401, B:L.403, B:G.429, B:S.430, B:Y.433, B:N.455, B:G.459, B:A.460 Water bridges: B:S.378, B:D.428, B:N.455, A:H.70 TPP.15: 26 residues within 4Å: Chain C: E.375, S.376, T.377, S.378, G.401, G.402, L.403, G.427, D.428, G.429, S.430, Y.433, N.455, T.457, Y.458, G.459, A.460, L.461 Chain D: N.23, P.24, G.25, S.26, E.47, H.70, N.77 Ligands: CA.12 17 PLIP interactions: 16 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:L.403, C:Y.433, C:L.461 Hydrogen bonds: C:S.376, C:T.377, C:T.377, C:S.378, C:G.401, C:L.403, C:G.429, C:S.430, C:G.459, C:A.460 Water bridges: C:S.378, C:D.428, C:D.428, D:H.70 TPP.20: 26 residues within 4Å: Chain C: N.23, P.24, G.25, S.26, E.47, H.70, N.77 Chain D: E.375, S.376, T.377, S.378, G.401, G.402, L.403, G.427, D.428, G.429, S.430, Y.433, N.455, T.457, Y.458, G.459, A.460, L.461 Ligands: CA.17 17 PLIP interactions: 16 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:L.403, D:Y.433, D:L.461 Hydrogen bonds: D:S.376, D:T.377, D:T.377, D:S.378, D:G.401, D:L.403, D:G.429, D:S.430, D:G.459, D:A.460 Water bridges: D:S.378, D:D.428, D:D.428, C:H.70

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bera, A.K. et al., Mechanism-based inactivation of benzoylformate decarboxylase, a thiamin diphosphate-dependent enzyme. J.Am.Chem.Soc. (2007)

Release Date

2006-12-19

Peptides

Benzoylformate decarboxylase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Benzoylformate decarboxylase

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