SMTL ID : 4jud.1

Crystal Structure of the Ser26Thr mutant of Benzoylformate Decarboxylase from Pseudomonas putida

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-tetramer

Ligands

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.1: 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, E.47, H.70, N.77 Ligands: CA.3, GOL.13 18 PLIP interactions: 17 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.433, A:L.461 Hydrogen bonds: A:S.376, 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 TZD.9: 26 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: GOL.5, CA.11 18 PLIP interactions: 1 interactions with chain A, 17 interactions with chain B Water bridges: A:H.70, B:D.428, B:N.455 Hydrophobic interactions: B:Y.433, B:L.461 Hydrogen bonds: B:S.376, 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 TZD.17: 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, E.47, H.70, N.77 Ligands: CA.19, GOL.29 18 PLIP interactions: 17 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:Y.433, C:L.461 Hydrogen bonds: C:S.376, 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 TZD.25: 26 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: GOL.21, CA.27 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.376, 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

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 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.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 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

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: D.428, N.455, T.457 Ligands: TZD.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.428, A:T.457, H2O.1 CA.11: 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.14 CA.19: 4 residues within 4Å: Chain C: D.428, N.455, T.457 Ligands: TZD.17 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.428, C:T.457, H2O.28 CA.27: 4 residues within 4Å: Chain D: D.428, N.455, T.457 Ligands: TZD.25 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.428, D:T.457, H2O.41

20 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: R.13, E.37, D.38 Ligand excluded by PLIP GOL.5: 5 residues within 4Å: Chain B: H.281, T.377, F.397, G.401 Ligands: TZD.9 Ligand excluded by PLIP GOL.6: 7 residues within 4Å: Chain A: W.86, P.276, D.301, L.303, E.304, R.307 Chain B: E.107 Ligand excluded by PLIP GOL.7: 5 residues within 4Å: Chain A: A.196, R.294, I.296, D.312 Chain C: H.178 Ligand excluded by PLIP GOL.8: 7 residues within 4Å: Chain A: A.102, G.105, V.106 Chain B: Y.288 Chain D: E.134, H.137, D.168 Ligand excluded by PLIP GOL.12: 3 residues within 4Å: Chain B: R.13, E.37, D.38 Ligand excluded by PLIP GOL.13: 5 residues within 4Å: Chain A: H.281, T.377, F.397, G.401 Ligands: TZD.1 Ligand excluded by PLIP GOL.14: 7 residues within 4Å: Chain A: E.107 Chain B: W.86, P.276, D.301, L.303, E.304, R.307 Ligand excluded by PLIP GOL.15: 5 residues within 4Å: Chain B: A.196, R.294, I.296, D.312 Chain D: H.178 Ligand excluded by PLIP GOL.16: 7 residues within 4Å: Chain A: Y.288 Chain B: A.102, G.105, V.106 Chain C: E.134, H.137, D.168 Ligand excluded by PLIP GOL.20: 3 residues within 4Å: Chain C: R.13, E.37, D.38 Ligand excluded by PLIP GOL.21: 5 residues within 4Å: Chain D: H.281, T.377, F.397, G.401 Ligands: TZD.25 Ligand excluded by PLIP GOL.22: 7 residues within 4Å: Chain C: W.86, P.276, D.301, L.303, E.304, R.307 Chain D: E.107 Ligand excluded by PLIP GOL.23: 5 residues within 4Å: Chain A: H.178 Chain C: A.196, R.294, I.296, D.312 Ligand excluded by PLIP GOL.24: 7 residues within 4Å: Chain B: E.134, H.137, D.168 Chain C: A.102, G.105, V.106 Chain D: Y.288 Ligand excluded by PLIP GOL.28: 3 residues within 4Å: Chain D: R.13, E.37, D.38 Ligand excluded by PLIP GOL.29: 5 residues within 4Å: Chain C: H.281, T.377, F.397, G.401 Ligands: TZD.17 Ligand excluded by PLIP GOL.30: 7 residues within 4Å: Chain C: E.107 Chain D: W.86, P.276, D.301, L.303, E.304, R.307 Ligand excluded by PLIP GOL.31: 5 residues within 4Å: Chain B: H.178 Chain D: A.196, R.294, I.296, D.312 Ligand excluded by PLIP GOL.32: 7 residues within 4Å: Chain A: E.134, H.137, D.168 Chain C: Y.288 Chain D: A.102, G.105, V.106 Ligand excluded by PLIP

Links

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Citation

Brodkin, H.R. et al., Crystal Structure of the Ser26Thr mutant of Benzoylformate Decarboxylase from Pseudomonas putida. To be Published

Release Date

2013-04-17

Peptides

Benzoylformate decarboxylase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
X

B
X

C
X

D
X

Benzoylformate decarboxylase