SMTL ID : 4mzx.1

Crystal Structure of Benzoylformate Decarboxylase Mutant T377L/A460Y

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.56 Å

Oligo State

homo-tetramer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: D.428, N.455, T.457 Ligands: TZD.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.428, A:T.457, H2O.1 CA.6: 4 residues within 4Å: Chain B: D.428, N.455, T.457 Ligands: TZD.9 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.428, B:T.457, H2O.18 CA.11: 4 residues within 4Å: Chain C: D.428, N.455, T.457 Ligands: TZD.14 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.428, C:T.457, H2O.36 CA.16: 4 residues within 4Å: Chain D: D.428, N.455, T.457 Ligands: TZD.19 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.428, D:T.457, H2O.53

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: I.192, L.193, A.196, R.294, I.296, D.312 Chain C: H.178 7 PLIP interactions: 2 interactions with chain C, 5 interactions with chain A Hydrogen bonds: C:H.178, A:R.294, A:R.294, A:D.312 Water bridges: C:H.178, A:D.312, A:A.313 GOL.3: 8 residues within 4Å: Chain A: L.43, W.439, Q.443, Y.444 Chain B: G.475, L.476, D.477, P.479 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:G.475, B:D.477, A:Q.443 Water bridges: B:L.476, B:D.477, A:Q.443 GOL.7: 7 residues within 4Å: Chain B: I.192, L.193, A.196, R.294, I.296, D.312 Chain D: H.178 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:R.294, B:R.294, B:D.312, D:H.178 Water bridges: B:D.312, B:A.313, D:H.178 GOL.8: 8 residues within 4Å: Chain A: G.475, L.476, D.477, P.479 Chain B: L.43, W.439, Q.443, Y.444 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.475, A:D.477, B:Q.443 Water bridges: A:L.476, A:D.477, B:Q.443 GOL.12: 7 residues within 4Å: Chain A: H.178 Chain C: I.192, L.193, A.196, R.294, I.296, D.312 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:R.294, C:R.294, A:H.178 Water bridges: C:D.312, C:A.313 GOL.13: 8 residues within 4Å: Chain C: L.43, W.439, Q.443, Y.444 Chain D: G.475, L.476, D.477, P.479 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:G.475, D:D.477, C:Q.443 Water bridges: D:L.476, C:Q.443 GOL.17: 7 residues within 4Å: Chain B: H.178 Chain D: I.192, L.193, A.196, R.294, I.296, D.312 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:R.294, D:R.294, B:H.178 Water bridges: D:D.312, D:A.313 GOL.18: 8 residues within 4Å: Chain C: G.475, L.476, D.477, P.479 Chain D: L.43, W.439, Q.443, Y.444 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:G.475, C:D.477, D:Q.443 Water bridges: C:L.476, D:Q.443

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.4: 28 residues within 4Å: Chain A: E.375, S.376, L.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, Y.460, L.461 Chain B: N.23, P.24, G.25, E.47, H.70, A.73, G.74, N.77, L.110 Ligands: CA.1 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:Y.433, A:Y.458, A:Y.458, A:L.461 Hydrogen bonds: A:L.377, A:S.378, A:S.378, A:G.401, A:L.403, A:G.429, A:S.430, A:Y.433, A:N.455, A:N.455, A:G.459, A:Y.460 Water bridges: A:D.428, A:S.430, A:S.430, A:N.455 TZD.9: 28 residues within 4Å: Chain A: N.23, P.24, G.25, E.47, H.70, A.73, G.74, N.77, L.110 Chain B: E.375, S.376, L.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, Y.460, L.461 Ligands: CA.6 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:Y.433, B:Y.458, B:Y.458, B:L.461 Hydrogen bonds: B:L.377, B:S.378, B:S.378, B:G.401, B:L.403, B:G.429, B:S.430, B:Y.433, B:N.455, B:N.455, B:G.459, B:Y.460 Water bridges: B:D.428, B:S.430, B:S.430, B:N.455 TZD.14: 28 residues within 4Å: Chain C: E.375, S.376, L.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, Y.460, L.461 Chain D: N.23, P.24, G.25, E.47, H.70, A.73, G.74, N.77, L.110 Ligands: CA.11 20 PLIP interactions: 19 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:L.377, C:S.378, C:S.378, C:G.401, C:L.403, C:G.429, C:S.430, C:N.455, C:N.455, C:G.459, C:Y.460 Water bridges: C:D.428, C:D.428, C:S.430, C:S.430, D:E.47 TZD.19: 28 residues within 4Å: Chain C: N.23, P.24, G.25, E.47, H.70, A.73, G.74, N.77, L.110 Chain D: E.375, S.376, L.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, Y.460, L.461 Ligands: CA.16 20 PLIP interactions: 19 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:L.377, D:S.378, D:S.378, D:G.401, D:L.403, D:G.429, D:S.430, D:N.455, D:N.455, D:G.459, D:Y.460 Water bridges: D:D.428, D:D.428, D:S.430, D:S.430, C:E.47

4 x NA: SODIUM ION(Non-functional Binders)

NA.5: 7 residues within 4Å: Chain A: N.117, L.118, R.120 Chain B: N.117, L.118, R.120 Ligands: NA.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.120 NA.10: 7 residues within 4Å: Chain A: N.117, L.118, R.120 Chain B: N.117, L.118, R.120 Ligands: NA.5 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.120 NA.15: 7 residues within 4Å: Chain C: N.117, L.118, R.120 Chain D: N.117, L.118, R.120 Ligands: NA.20 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.117 NA.20: 7 residues within 4Å: Chain C: N.117, L.118, R.120 Chain D: N.117, L.118, R.120 Ligands: NA.15 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.117

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Andrews, F.H. et al., Mechanistic and structural insight to an evolved benzoylformate decarboxylase with enhanced activity towards pyruvate. To be Published

Release Date

2015-04-01

Peptides

Benzoylformate decarboxlyase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Benzoylformate decarboxlyase