SMTL ID : 4mpp.1

Crystal Structure of Benzoylformate Decarboxylase Mutant H281Y/T377P/F397T/A460I

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-tetramer

Ligands

8 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.1 CA.2: 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.11, H2O.13, H2O.14, H2O.17 CA.10: 4 residues within 4Å: Chain B: D.428, N.455, T.457 Ligands: TZD.14 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.428, B:T.457, H2O.23 CA.11: 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.33, H2O.35, H2O.36, H2O.38 CA.19: 4 residues within 4Å: Chain C: D.428, N.455, T.457 Ligands: TZD.23 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.428, C:T.457, H2O.45 CA.20: 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.55, H2O.57, H2O.58, H2O.60 CA.28: 4 residues within 4Å: Chain D: D.428, N.455, T.457 Ligands: TZD.32 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.428, D:T.457, H2O.66 CA.29: 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.76, H2O.79, H2O.80, H2O.82

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

NA.3: 1 residues within 4Å: Chain A: D.347 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.347 NA.4: 7 residues within 4Å: Chain A: N.117, L.118, R.120 Chain B: N.117, L.118, R.120 Ligands: NA.13 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.117 NA.12: 1 residues within 4Å: Chain B: D.347 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.347 NA.13: 7 residues within 4Å: Chain A: N.117, L.118, R.120 Chain B: N.117, L.118, R.120 Ligands: NA.4 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.120 NA.21: 1 residues within 4Å: Chain C: D.347 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.347 NA.22: 7 residues within 4Å: Chain C: N.117, L.118, R.120 Chain D: N.117, L.118, R.120 Ligands: NA.31 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.117 NA.30: 1 residues within 4Å: Chain D: D.347 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.347 NA.31: 7 residues within 4Å: Chain C: N.117, L.118, R.120 Chain D: N.117, L.118, R.120 Ligands: NA.22 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C: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: 27 residues within 4Å: Chain A: E.375, S.376, P.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, I.460, L.461 Chain B: N.23, P.24, G.25, E.47, H.70, A.73, G.74, N.77 Ligands: CA.1 19 PLIP interactions: 18 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.433, A:L.461 Hydrogen bonds: 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:T.457, A:G.459, A:I.460 Water bridges: A:S.376, A:S.378, A:D.428, A:N.455, B:H.70 TZD.14: 27 residues within 4Å: Chain A: N.23, P.24, G.25, E.47, H.70, A.73, G.74, N.77 Chain B: E.375, S.376, P.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, I.460, L.461 Ligands: CA.10 19 PLIP interactions: 18 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.433, B:L.461 Hydrogen bonds: 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:T.457, B:G.459, B:I.460 Water bridges: B:S.376, B:S.378, B:D.428, B:N.455, A:H.70 TZD.23: 27 residues within 4Å: Chain C: E.375, S.376, P.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, I.460, L.461 Chain D: N.23, P.24, G.25, E.47, H.70, A.73, G.74, N.77 Ligands: CA.19 17 PLIP interactions: 16 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:Y.433, C:L.461 Hydrogen bonds: C:S.378, C:S.378, C:G.401, C:L.403, C:G.429, C:S.430, C:T.457, C:T.457, C:G.459, C:I.460 Water bridges: C:S.376, C:S.378, C:D.428, C:N.455, D:H.70 TZD.32: 27 residues within 4Å: Chain C: N.23, P.24, G.25, E.47, H.70, A.73, G.74, N.77 Chain D: E.375, S.376, P.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, I.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:S.378, D:S.378, D:G.401, D:L.403, D:G.429, D:S.430, D:N.455, D:T.457, D:T.457, D:G.459, D:I.460 Water bridges: D:S.376, D:S.378, D:D.428, D:N.455, C:H.70

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 8 residues within 4Å: Chain A: L.43, W.439, Q.443, Y.444 Chain B: G.475, L.476, D.477, P.479 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:G.475, B:D.477 Water bridges: B:D.477, A:Q.443, A:Q.443 GOL.7: 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.8: 8 residues within 4Å: Chain A: A.102, G.105, V.106 Chain B: Y.288 Chain D: A.133, E.134, H.137, D.168 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain A Hydrogen bonds: D:H.137, D:D.168 Water bridges: D:S.131, A:G.105, A:G.105, A:V.106 GOL.15: 8 residues within 4Å: Chain A: G.475, L.476, D.477, P.479 Chain B: L.43, W.439, Q.443, Y.444 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Water bridges: B:Q.443, B:Q.443, A:D.477 Hydrogen bonds: A:G.475, A:D.477 GOL.16: 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: 2 interactions with chain D, 4 interactions with chain B Hydrogen bonds: D:H.178, B:R.294, B:R.294, B:D.312 Water bridges: D:H.178, B:D.312 GOL.17: 8 residues within 4Å: Chain A: Y.288 Chain B: A.102, G.105, V.106 Chain C: A.133, E.134, H.137, D.168 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:H.137, C:D.168 Water bridges: C:S.131, B:G.105, B:G.105, B:V.106 GOL.24: 8 residues within 4Å: Chain C: L.43, W.439, Q.443, Y.444 Chain D: G.475, L.476, D.477, P.479 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:G.475, D:D.477 Water bridges: C:Q.443, C:Q.443 GOL.25: 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: 1 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:H.178, C:R.294, C:R.294 Water bridges: C:D.312 GOL.26: 8 residues within 4Å: Chain B: A.133, E.134, H.137, D.168 Chain C: A.102, G.105, V.106 Chain D: Y.288 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:H.137 Water bridges: B:S.131, C:G.105, C:G.105, C:V.106 GOL.33: 8 residues within 4Å: Chain C: G.475, L.476, D.477, P.479 Chain D: L.43, W.439, Q.443, Y.444 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:G.475, C:D.477 Water bridges: D:Q.443, D:Q.443 GOL.34: 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.35: 8 residues within 4Å: Chain A: A.133, E.134, H.137, D.168 Chain C: Y.288 Chain D: A.102, G.105, V.106 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain A Water bridges: D:G.105, D:G.105, D:V.106, A:S.131 Hydrogen bonds: A:H.137

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

CL.9: 3 residues within 4Å: Chain A: N.186, D.187 Chain C: R.184 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain B: N.186, D.187 Chain D: R.184 Ligand excluded by PLIP CL.27: 3 residues within 4Å: Chain A: R.184 Chain C: N.186, D.187 Ligand excluded by PLIP CL.36: 3 residues within 4Å: Chain B: R.184 Chain D: N.186, D.187 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Andrews, F.H. et al., A pseudo study of thiamin diphosphate-dependent decarboxylases. To be Published

Release Date

2015-03-18

Peptides

Benzoylformate decarboxylase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Benzoylformate decarboxylase