SMTL ID : 4mpj.1

Phosphorylation of an active site threonine in the benzyolformate decarboxylase mutant S26T by phosphonate inactivation

Coordinates

PDB Format Compare

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: TPP.4 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.10, H2O.18, H2O.21 CA.9: 4 residues within 4Å: Chain B: D.428, N.455, T.457 Ligands: TPP.12 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.25, H2O.31, H2O.39, H2O.43 CA.17: 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.44 CA.19: 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.47, H2O.53, H2O.61, H2O.64 CA.25: 4 residues within 4Å: Chain D: D.428, N.455, T.457 Ligands: TPP.28 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.428, D:T.457, H2O.66 CA.27: 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.68, H2O.74, H2O.82, H2O.86

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 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.2 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.18: 7 residues within 4Å: Chain C: N.117, L.118, R.120 Chain D: N.117, L.118, R.120 Ligands: MG.26 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.26: 7 residues within 4Å: Chain C: N.117, L.118, R.120 Chain D: N.117, L.118, R.120 Ligands: MG.18 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.4: 26 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, T.26, 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:G.401, A:L.403, A:G.427, 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.12: 26 residues within 4Å: Chain A: N.23, P.24, G.25, T.26, 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.9 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:G.401, B:L.403, B:G.427, 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: 26 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, T.26, E.47, H.70, N.77 Ligands: CA.17 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:G.401, C:L.403, C:G.427, 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.28: 26 residues within 4Å: Chain C: N.23, P.24, G.25, T.26, 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.25 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:G.401, D:L.403, D:G.427, 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.5: 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.6: 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 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain D Water bridges: A:G.105, A:G.105, A:V.106, D:S.131 Hydrogen bonds: D:H.137, D:D.168, D:D.168 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 Water bridges: A:D.312, C:H.178, C:H.178 GOL.13: 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: 2 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:Q.443, A:G.475, A:D.477 Water bridges: B:Q.443, A:L.476, A:D.477 GOL.14: 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 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:H.137, C:D.168, C:D.168 Water bridges: C:S.131, B:G.105, B:G.105, B:V.106 GOL.15: 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 Water bridges: B:D.312, D:H.178, D:H.178 GOL.21: 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.22: 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 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain B Water bridges: C:G.105, C:G.105, C:V.106, B:S.131 Hydrogen bonds: B:H.137, B:D.168 GOL.23: 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: 3 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:R.294, C:R.294 Water bridges: C:D.312, A:H.178, A:H.178 GOL.29: 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: 2 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:Q.443, C:G.475, C:D.477 Water bridges: D:Q.443, C:L.476 GOL.30: 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 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain D Hydrogen bonds: A:H.137, A:D.168 Water bridges: A:S.131, D:G.105, D:G.105, D:V.106 GOL.31: 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: 3 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:R.294, D:R.294 Water bridges: D:D.312, B:H.178, B:H.178

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.16: 3 residues within 4Å: Chain B: N.186, D.187 Chain D: R.184 Ligand excluded by PLIP CL.24: 3 residues within 4Å: Chain A: R.184 Chain C: N.186, D.187 Ligand excluded by PLIP CL.32: 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., Phosphorylation of an active site threonine in the benzyolformate decarboxylase mutant S26T by phosphonate inactivation. 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