SMTL ID : 1mcz.3 (3 other biounits)

BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA COMPLEXED WITH AN INHIBITOR, R-MANDELATE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-tetramer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.428, N.455, T.457 Ligands: TPP.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.428, A:T.457, H2O.1 MG.2: 6 residues within 4Å: Chain A: N.117, L.118, R.120 Chain B: N.117, L.118, R.120 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Metal complexes: B:N.117, B:L.118, B:R.120, A:L.118, A:R.120 MG.5: 5 residues within 4Å: Chain B: D.428, N.455, T.457, G.459 Ligands: TPP.6 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.428, B:T.457, H2O.5 MG.8: 4 residues within 4Å: Chain C: D.428, N.455, T.457 Ligands: TPP.9 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.428, C:T.457, H2O.9 MG.11: 4 residues within 4Å: Chain D: D.428, N.455, T.457 Ligands: TPP.13 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.428, D:T.457, H2O.13 MG.12: 6 residues within 4Å: Chain C: N.117, L.118, R.120 Chain D: N.117, L.118, R.120 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain D Metal complexes: C:N.117, C:L.118, C:R.120, D:N.117, D:L.118, D:R.120

4 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.3: 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, E.47, H.70, N.77 Ligands: MG.1, RMN.4 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:Y.433, A:L.461 Hydrogen bonds: A:T.377, A:S.378, A:S.378, A:G.401, A:L.403, A:G.427, A:G.429, A:S.430, A:S.430, A:N.455, A:G.459, A:A.460 Water bridges: A:S.376, A:S.378, A:D.428, A:N.455 TPP.6: 26 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: MG.5, RMN.7 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:Y.433, B:L.461 Hydrogen bonds: B:T.377, B:S.378, B:S.378, B:G.401, B:L.403, B:G.427, B:G.429, B:S.430, B:S.430, B:N.455, B:G.459, B:A.460 Water bridges: B:S.376, B:S.378, B:D.428, B:D.428 TPP.9: 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, E.47, H.70, N.77 Ligands: MG.8, RMN.10 18 PLIP interactions: 18 interactions with chain C Hydrophobic interactions: C:Y.433, C:L.461 Hydrogen bonds: C:T.377, C:T.377, C:S.378, C:S.378, C:G.401, C:L.403, C:G.427, C:G.429, C:S.430, C:Y.433, C:N.455, C:T.457, C:G.459, C:A.460 Water bridges: C:D.428, C:N.455 TPP.13: 26 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: MG.11, RMN.14 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:Y.433, D:L.461 Hydrogen bonds: D:T.377, D:T.377, D:S.378, D:S.378, D:G.401, D:L.403, D:G.427, D:G.429, D:S.430, D:Y.433, D:N.455, D:T.457, D:G.459, D:A.460 Water bridges: D:D.428, D:N.455

4 x RMN: (R)-MANDELIC ACID(Non-covalent)

RMN.4: 10 residues within 4Å: Chain A: H.281, T.377, F.397, G.401, L.461 Chain B: G.25, S.26, H.70, L.110 Ligands: TPP.3 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:T.377, A:F.397 Hydrogen bonds: A:G.401, B:S.26 Salt bridges: A:H.281, B:H.70 RMN.7: 11 residues within 4Å: Chain A: G.25, S.26, H.70, L.110 Chain B: H.281, T.377, F.397, G.401, L.461, F.464 Ligands: TPP.6 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:T.377, B:F.397 Hydrogen bonds: B:G.401, A:S.26 Salt bridges: B:H.281, A:H.70 RMN.10: 11 residues within 4Å: Chain C: H.281, T.377, F.397, G.401, L.461, F.464 Chain D: G.25, S.26, H.70, L.110 Ligands: TPP.9 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:T.377, C:F.397 Hydrogen bonds: C:G.401, D:S.26 Salt bridges: C:H.281, D:H.70 RMN.14: 10 residues within 4Å: Chain C: G.25, S.26, H.70, L.110 Chain D: H.281, T.377, F.397, G.401, L.461 Ligands: TPP.13 6 PLIP interactions: 2 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:S.26, D:G.401 Salt bridges: C:H.70, D:H.281 Hydrophobic interactions: D:T.377, D:F.397

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

POLOVNIKOVA, E.S. et al., Structural and Kinetic Analysis of Catalysis by a ThiaminDiphosphate-Dependent Enzyme, Benzoylformate Decarboxylase. Biochemistry (2003)

Release Date

2003-02-25

Peptides

BENZOYLFORMATE DECARBOXYLASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
I

B
J

C
K

D
L

BENZOYLFORMATE DECARBOXYLASE

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