SMTL ID : 2v3w.1

Crystal structure of the benzoylformate decarboxylase variant L461A from Pseudomonas putida

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.428, N.455, T.457, G.459 Ligands: TPP.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.428, A:T.457, H2O.9 MG.2: 6 residues within 4Å: Chain A: N.117, L.118, R.120 Chain C: N.117, L.118, R.120 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain C Metal complexes: A:N.117, A:L.118, A:R.120, C:N.117, C:L.118, C:R.120 MG.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.18 MG.6: 6 residues within 4Å: Chain B: N.117, L.118, R.120 Chain D: N.117, L.118, R.120 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain D Metal complexes: B:N.117, B:L.118, B:R.120, D:L.118, D:R.120 MG.9: 4 residues within 4Å: Chain C: D.428, N.455, T.457 Ligands: TPP.11 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.428, C:T.457, H2O.27 MG.12: 4 residues within 4Å: Chain D: D.428, N.455, T.457 Ligands: TPP.14 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.428, D:T.457, H2O.36

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 7 residues within 4Å: Chain A: G.25, S.26, H.70, L.110 Chain C: H.281, F.464 Ligands: TPP.11 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:S.26 Salt bridges: A:H.70, C:H.281 SO4.7: 7 residues within 4Å: Chain B: G.25, S.26, H.70, L.110 Chain D: H.281, F.464 Ligands: TPP.14 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:S.26 Salt bridges: B:H.70, D:H.281 SO4.10: 7 residues within 4Å: Chain A: H.281, F.464 Chain C: G.25, S.26, H.70, L.110 Ligands: TPP.4 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:S.26 Salt bridges: C:H.70, A:H.281 Water bridges: A:A.460 SO4.13: 7 residues within 4Å: Chain B: H.281, F.464 Chain D: G.25, S.26, H.70, L.110 Ligands: TPP.8 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:S.26 Salt bridges: D:H.70, B:H.281

4 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.4: 24 residues within 4Å: Chain A: E.375, S.376, T.377, S.378, G.401, L.403, G.427, D.428, G.429, S.430, Y.433, N.455, T.457, Y.458, G.459, A.460 Chain C: N.23, P.24, G.25, E.47, H.70, N.77 Ligands: MG.1, SO4.10 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:Y.433 Hydrogen bonds: A:S.376, A:T.377, 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: 27 residues within 4Å: 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 Chain D: N.23, P.24, G.25, E.47, H.70, A.73, G.74, N.77 Ligands: MG.5, SO4.13 18 PLIP interactions: 2 interactions with chain D, 16 interactions with chain B Hydrophobic interactions: D:A.73, B:Y.433, B:Y.458, B:Y.458 Water bridges: D:E.47, B:D.428, B:D.428 Hydrogen bonds: B:S.376, B:T.377, B:T.377, B:S.378, B:G.401, B:L.403, B:G.429, B:S.430, B:N.455, B:G.459, B:A.460 TPP.11: 25 residues within 4Å: Chain A: N.23, P.24, G.25, E.47, H.70, N.77 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 Ligands: SO4.3, MG.9 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:L.403, C:Y.433 Hydrogen bonds: C:S.376, C:T.377, C:T.377, C:S.378, C:S.378, C:G.401, C:L.403, C:G.429, C:S.430, C:Y.433, C:N.455, C:G.459, C:A.460 Water bridges: C:D.428, C:D.428 TPP.14: 25 residues within 4Å: Chain B: 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 Ligands: SO4.7, MG.12 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:Y.433, D:Y.458, D:Y.458 Hydrogen bonds: D:S.376, D:T.377, D:T.377, D:S.378, D:S.378, D:G.401, D:L.403, D:G.429, D:S.430, D:N.455, D:G.459, D:A.460 Water bridges: D:D.428, D:D.428

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gocke, D. et al., Rational Protein Design of Thdp-Dependent Enzymes-Engineering Stereoselectivity. Chembiochem (2008)

Release Date

2008-01-22

Peptides

BENZOYLFORMATE DECARBOXYLASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

BENZOYLFORMATE DECARBOXYLASE