SMTL ID : 1q6z.1

HIGH RESOLUTION STRUCTURE OF E28A MUTANT BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA COMPLEXED WITH THIAMIN THIAZOLONE DIPHOSPHATE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.00 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: TZD.5 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.428, A:T.457 CA.3: 1 residues within 4Å: Chain A: D.364 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.364, H2O.7, H2O.12 CA.4: 1 residues within 4Å: Chain A: A.416 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:A.416, H2O.7, H2O.7, H2O.18, H2O.18 CA.7: 4 residues within 4Å: Chain B: D.428, N.455, T.457 Ligands: TZD.10 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.428, B:T.457 CA.8: 1 residues within 4Å: Chain B: D.364 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.364, H2O.29, H2O.35 CA.9: 1 residues within 4Å: Chain B: A.416 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:A.416, H2O.30, H2O.30, H2O.40, H2O.41 CA.12: 4 residues within 4Å: Chain C: D.428, N.455, T.457 Ligands: TZD.15 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.428, C:T.457 CA.13: 1 residues within 4Å: Chain C: D.364 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.364, H2O.52, H2O.58 CA.14: 1 residues within 4Å: Chain C: A.416 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:A.416, H2O.52, H2O.53, H2O.63, H2O.64 CA.17: 4 residues within 4Å: Chain D: D.428, N.455, T.457 Ligands: TZD.20 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.428, D:T.457 CA.18: 1 residues within 4Å: Chain D: D.364 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.364, H2O.74, H2O.80 CA.19: 1 residues within 4Å: Chain D: A.416 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:A.416, H2O.75, H2O.75, H2O.85, H2O.86

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, H.70, N.77 Ligands: CA.2 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.433, A:L.461 Hydrogen bonds: A:T.377, A:S.378, A:G.401, A:L.403, A:G.429, A:S.430, A:S.430, A:Y.433, A:N.455, A:N.455, A:G.459, A:A.460 TZD.10: 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.7 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:Y.433, B:L.461 Hydrogen bonds: B:T.377, B:S.378, B:G.401, B:L.403, B:G.429, B:S.430, B:S.430, B:Y.433, B:N.455, B:N.455, B:G.459, B:A.460 TZD.15: 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.12 15 PLIP interactions: 14 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:Y.433, C:L.461 Hydrogen bonds: C:T.377, C:T.377, C:S.378, C:G.401, C:L.403, C:G.429, C:S.430, C:S.430, C:N.455, C:N.455, C:G.459, C:A.460 Water bridges: D:E.47 TZD.20: 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.17 15 PLIP interactions: 14 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:Y.433, D:L.461 Hydrogen bonds: D:T.377, D:T.377, D:S.378, D:G.401, D:L.403, D:G.429, D:S.430, D:S.430, D:N.455, D:N.455, D:G.459, D:A.460 Water bridges: C:E.47

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bera, A.K. et al., High Resolution Structure of E28A Mutant Benzoylformate Decarboxylase from Pseudomonas Putida Complexed with Thiamin Thiazolone Diphosphate. To be Published

Release Date

2004-11-23

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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