SMTL ID : 1bfd.1

BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

8 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: D.428, N.455, T.457 Ligands: TPP.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.428, A:T.457, H2O.1 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.158, H2O.170, H2O.309, H2O.310 CA.5: 4 residues within 4Å: Chain B: D.428, N.455, T.457 Ligands: TPP.8 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.428, B:T.457, H2O.347 CA.7: 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.504, H2O.516, H2O.655, H2O.656 CA.9: 4 residues within 4Å: Chain C: D.428, N.455, T.457 Ligands: TPP.12 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.428, C:T.457, H2O.693 CA.11: 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.850, H2O.862, H2O.1001, H2O.1002 CA.13: 4 residues within 4Å: Chain D: D.428, N.455, T.457 Ligands: TPP.16 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.428, D:T.457, H2O.1039 CA.15: 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.1196, H2O.1208, H2O.1347, H2O.1348

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 7 residues within 4Å: Chain A: N.117, L.118, R.120 Chain B: N.117, L.118, R.120 Ligands: MG.6 5 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:L.118, B:R.120, A:L.118, A:R.120, H2O.270 MG.6: 7 residues within 4Å: Chain A: N.117, L.118, R.120 Chain B: N.117, L.118, R.120 Ligands: MG.2 5 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:L.118, B:R.120, A:L.118, A:R.120, H2O.270 MG.10: 7 residues within 4Å: Chain C: N.117, L.118, R.120 Chain D: N.117, L.118, R.120 Ligands: MG.14 5 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: D:L.118, D:R.120, C:L.118, C:R.120, H2O.962 MG.14: 7 residues within 4Å: Chain C: N.117, L.118, R.120 Chain D: N.117, L.118, R.120 Ligands: MG.10 5 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: D:L.118, D:R.120, C:L.118, C:R.120, H2O.962

4 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.4: 25 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, E.47, H.70, N.77 Ligands: CA.1 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:Y.433, A:Y.458, A:Y.458, A:L.461 Hydrogen bonds: A:S.376, A:T.377, A:S.378, A:G.401, A:L.403, A:G.427, A:G.429, A:S.430, A:Y.433, A:N.455, A:G.459, A:A.460 Water bridges: A:D.428, A:D.428 TPP.8: 25 residues within 4Å: Chain A: N.23, P.24, G.25, 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.5 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:Y.433, B:Y.458, B:Y.458, B:L.461 Hydrogen bonds: B:S.376, B:T.377, B:S.378, B:G.401, B:L.403, B:G.427, B:G.429, B:S.430, B:Y.433, B:N.455, B:G.459, B:A.460 Water bridges: B:D.428, B:D.428 TPP.12: 25 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, E.47, H.70, N.77 Ligands: CA.9 19 PLIP interactions: 18 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:Y.433, C:Y.458, C:Y.458, 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.427, C:G.429, C:S.430, C:N.455, C:G.459, C:A.460 Water bridges: C:D.428, C:D.428, D:E.47 TPP.16: 25 residues within 4Å: Chain C: N.23, P.24, G.25, 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.13 19 PLIP interactions: 18 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:Y.433, D:Y.458, D:Y.458, 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.427, D:G.429, D:S.430, D:N.455, D:G.459, D:A.460 Water bridges: D:D.428, D:D.428, C:E.47

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hasson, M.S. et al., The crystal structure of benzoylformate decarboxylase at 1.6 A resolution: diversity of catalytic residues in thiamin diphosphate-dependent enzymes. Biochemistry (1998)

Release Date

1998-06-24

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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