SMTL ID : 4qel.1

Crystal Structure of Benzoylformate Decarboxylase Mutant H70A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.43 Å

Oligo State

homo-tetramer

Ligands

12 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: D.428, N.455, T.457 Ligands: TZD.5 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.428, A:T.457, H2O.2 CA.2: 1 residues within 4Å: Chain A: D.364 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.364, H2O.3, H2O.9, H2O.19 CA.6: 1 residues within 4Å: Chain A: D.347 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.347, H2O.4, H2O.6, H2O.7, H2O.10 CA.7: 4 residues within 4Å: Chain B: D.428, N.455, T.457 Ligands: TZD.11 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.428, B:T.457, H2O.21 CA.8: 1 residues within 4Å: Chain B: D.364 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.364, H2O.22, H2O.28, H2O.38 CA.12: 1 residues within 4Å: Chain B: D.347 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.347, H2O.23, H2O.26, H2O.26, H2O.30 CA.13: 4 residues within 4Å: Chain C: D.428, N.455, T.457 Ligands: TZD.17 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.428, C:T.457, H2O.41 CA.14: 1 residues within 4Å: Chain C: D.364 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.364, H2O.42, H2O.47, H2O.57 CA.18: 1 residues within 4Å: Chain C: D.347 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:D.347, H2O.42, H2O.45, H2O.45, H2O.49 CA.19: 4 residues within 4Å: Chain D: D.428, N.455, T.457 Ligands: TZD.23 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.428, D:T.457, H2O.60 CA.20: 1 residues within 4Å: Chain D: D.364 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.364, H2O.61, H2O.66, H2O.77 CA.24: 1 residues within 4Å: Chain D: D.347 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:D.347, H2O.62, H2O.64, H2O.64, H2O.68

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 3 residues within 4Å: Chain A: N.186, D.187 Chain C: R.184 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain B: N.186, D.187 Chain D: R.184 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain A: R.184 Chain C: N.186, D.187 Ligand excluded by PLIP CL.21: 3 residues within 4Å: Chain B: R.184 Chain D: N.186, D.187 Ligand excluded by PLIP

4 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 7 residues within 4Å: Chain A: N.117, L.118, R.120 Chain B: N.117, L.118, R.120 Ligands: MG.10 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.10: 7 residues within 4Å: Chain A: N.117, L.118, R.120 Chain B: N.117, L.118, R.120 Ligands: MG.4 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.16: 7 residues within 4Å: Chain C: N.117, L.118, R.120 Chain D: N.117, L.118, R.120 Ligands: MG.22 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 MG.22: 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 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 TZD: 2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL-2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYL TRIHYDROGEN DIPHOSPHATE(Non-covalent)

TZD.5: 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, A.70, N.77 Ligands: CA.1 21 PLIP interactions: 19 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.433, A:L.461, B:A.70 Hydrogen bonds: A:S.376, A:T.377, 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:Y.433, A:N.455, A:G.459, A:A.460 Water bridges: A:D.428, A:N.455, B:S.26 TZD.11: 25 residues within 4Å: Chain A: N.23, P.24, G.25, E.47, A.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 21 PLIP interactions: 19 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.433, B:L.461, A:A.70 Hydrogen bonds: B:S.376, B:T.377, 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:Y.433, B:N.455, B:G.459, B:A.460 Water bridges: B:D.428, B:N.455, A:S.26 TZD.17: 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, A.70, N.77 Ligands: CA.13 21 PLIP interactions: 19 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:Y.433, C:L.461, D:A.70 Hydrogen bonds: C:S.376, C:T.377, 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:S.430, C:N.455, C:G.459, C:A.460 Water bridges: C:D.428, C:D.428, D:S.26 TZD.23: 25 residues within 4Å: Chain C: N.23, P.24, G.25, E.47, A.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.19 20 PLIP interactions: 18 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:Y.433, D:L.461, C:A.70 Hydrogen bonds: D:S.376, D:T.377, 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:S.430, D:G.459, D:A.460 Water bridges: D:D.428, D:D.428, C:S.26

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Andrews, F.H. et al., Structural investigation of benzoylformate decarboxylase active site variants. To be Published

Release Date

2015-05-20

Peptides

Benzoylformate decarboxylase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Benzoylformate decarboxylase