SMTL ID : 4mpr.1

Benzoylformate Decarboxylase: Is the tetramer vital for activity?

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 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: TPP.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.428, A:T.457, H2O.1 CA.3: 1 residues within 4Å: Chain A: D.364 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.364, H2O.4, H2O.6, H2O.8, H2O.22 CA.6: 7 residues within 4Å: Chain A: N.117, L.118, R.120 Chain B: N.117, L.118, R.120 Ligands: CA.15 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Metal complexes: B:N.117, B:L.118, B:R.120, A:N.117, A:L.118, A:R.120 CA.10: 4 residues within 4Å: Chain B: D.428, N.455, T.457 Ligands: TPP.11 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.428, B:T.457, H2O.24 CA.12: 1 residues within 4Å: Chain B: D.364 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.364, H2O.26, H2O.29, H2O.30, H2O.45 CA.15: 7 residues within 4Å: Chain A: N.117, L.118, R.120 Chain B: N.117, L.118, R.120 Ligands: CA.6 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Metal complexes: B:N.117, B:L.118, B:R.120, A:N.117, A:L.118, A:R.120 CA.19: 4 residues within 4Å: Chain C: D.428, N.455, T.457 Ligands: TPP.20 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.428, C:T.457, H2O.46 CA.21: 1 residues within 4Å: Chain C: D.364 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:D.364, H2O.49, H2O.51, H2O.53, H2O.67 CA.24: 7 residues within 4Å: Chain C: N.117, L.118, R.120 Chain D: N.117, L.118, R.120 Ligands: CA.33 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 CA.28: 4 residues within 4Å: Chain D: D.428, N.455, T.457 Ligands: TPP.29 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.428, D:T.457, H2O.69 CA.30: 1 residues within 4Å: Chain D: D.364 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:D.364, H2O.71, H2O.74, H2O.75, H2O.90 CA.33: 7 residues within 4Å: Chain C: N.117, L.118, R.120 Chain D: N.117, L.118, R.120 Ligands: CA.24 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.2: 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.1 18 PLIP interactions: 17 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.433, A:L.461 Hydrogen bonds: A:T.377, A:T.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:T.457, A:G.459, A:A.460 Water bridges: A:D.428, A:N.455, B:H.70 TPP.11: 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.10 18 PLIP interactions: 17 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.433, B:L.461 Hydrogen bonds: B:T.377, B:T.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:T.457, B:G.459, B:A.460 Water bridges: B:D.428, B:N.455, A:H.70 TPP.20: 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.19 18 PLIP interactions: 17 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:T.377, C:S.378, C:S.378, C:G.401, C:L.403, C:G.429, C:S.430, C:N.455, C:T.457, C:G.459, C:A.460 Water bridges: C:D.428, C:N.455, D:H.70 TPP.29: 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.28 18 PLIP interactions: 17 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:T.377, D:S.378, D:S.378, D:G.401, D:L.403, D:G.429, D:S.430, D:N.455, D:T.457, D:G.459, D:A.460 Water bridges: D:D.428, D:N.455, C:H.70

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: I.192, L.193, A.196, R.294, I.296, D.312 Chain C: H.178 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:R.294, A:R.294, A:D.312, C:H.178 Water bridges: A:D.312, C:H.178 GOL.5: 3 residues within 4Å: Chain A: P.392, E.417, R.420 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:P.392, A:R.420, A:R.420 Water bridges: A:R.62, A:R.62, A:E.417 GOL.7: 8 residues within 4Å: Chain A: G.475, L.476, D.477, P.479 Chain B: L.43, W.439, Q.443, Y.444 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.475, A:D.477, A:D.477 Water bridges: A:D.477, A:D.477, B:Q.443, B:Q.443 GOL.13: 7 residues within 4Å: Chain B: I.192, L.193, A.196, R.294, I.296, D.312 Chain D: H.178 6 PLIP interactions: 4 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, D:H.178 GOL.14: 3 residues within 4Å: Chain B: P.392, E.417, R.420 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:P.392, B:R.420, B:R.420 Water bridges: B:R.62, B:R.62, B:E.417 GOL.16: 8 residues within 4Å: Chain A: L.43, W.439, Q.443, Y.444 Chain B: G.475, L.476, D.477, P.479 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:G.475, B:D.477, B:D.477 Water bridges: B:D.477, B:D.477, A:Q.443, A:Q.443 GOL.22: 7 residues within 4Å: Chain A: H.178 Chain C: I.192, L.193, A.196, R.294, I.296, D.312 4 PLIP interactions: 3 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 GOL.23: 3 residues within 4Å: Chain C: P.392, E.417, R.420 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:P.392, C:R.420, C:R.420 Water bridges: C:R.62, C:E.417 GOL.25: 8 residues within 4Å: Chain C: G.475, L.476, D.477, P.479 Chain D: L.43, W.439, Q.443, Y.444 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain C Water bridges: D:Q.443, D:Q.443, C:D.477 Hydrogen bonds: C:G.475, C:D.477, C:D.477 GOL.31: 7 residues within 4Å: Chain B: H.178 Chain D: I.192, L.193, A.196, R.294, I.296, D.312 4 PLIP interactions: 3 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 GOL.32: 3 residues within 4Å: Chain D: P.392, E.417, R.420 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:P.392, D:R.420, D:R.420 Water bridges: D:R.62, D:E.417 GOL.34: 8 residues within 4Å: Chain C: L.43, W.439, Q.443, Y.444 Chain D: G.475, L.476, D.477, P.479 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:G.475, D:D.477, D:D.477 Water bridges: D:D.477, C:Q.443, C:Q.443

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

CL.8: 3 residues within 4Å: Chain A: N.186, D.187 Chain C: R.184 Ligand excluded by PLIP CL.17: 3 residues within 4Å: Chain B: N.186, D.187 Chain D: R.184 Ligand excluded by PLIP CL.26: 3 residues within 4Å: Chain A: R.184 Chain C: N.186, D.187 Ligand excluded by PLIP CL.35: 3 residues within 4Å: Chain B: R.184 Chain D: N.186, D.187 Ligand excluded by PLIP

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

NA.9: 2 residues within 4Å: Chain A: E.141 Chain D: G.105 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.141 NA.18: 2 residues within 4Å: Chain B: E.141 Chain C: G.105 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.105 NA.27: 2 residues within 4Å: Chain B: G.105 Chain C: E.141 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.141 NA.36: 2 residues within 4Å: Chain A: G.105 Chain D: E.141 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.141

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Andrews, F.H. et al., Perturbation of the monomer-monomer interfaces of the benzoylformate decarboxylase tetramer. Biochemistry (2014)

Release Date

2014-08-27

Peptides

Benzoylformate decarboxylase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Benzoylformate decarboxylase