SMTL ID : 4k9l.1

Crystal Structure of the His281Thr mutant of Benzoylformate Decarboxylase from Pseudomonas putida

Coordinates

PDB Format

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.374, S.375, T.376, S.377, G.400, G.401, L.402, G.426, D.427, G.428, S.429, Y.432, N.454, T.456, Y.457, G.458, A.459, L.460 Chain B: N.22, P.23, G.24, E.46, H.69, N.76 Ligands: CA.2, EDO.6 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.432, A:L.460 Hydrogen bonds: A:T.376, A:T.376, A:S.377, A:G.400, A:L.402, A:G.426, A:G.428, A:S.429, A:S.429, A:G.458, A:A.459 Water bridges: A:D.427, A:N.454, B:H.69 TZD.12: 26 residues within 4Å: Chain A: N.22, P.23, G.24, E.46, H.69, N.76 Chain B: E.374, S.375, T.376, S.377, G.400, G.401, L.402, G.426, D.427, G.428, S.429, Y.432, N.454, T.456, Y.457, G.458, A.459, L.460 Ligands: CA.13, EDO.17 16 PLIP interactions: 15 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.432, B:L.460 Hydrogen bonds: B:T.376, B:T.376, B:S.377, B:G.400, B:L.402, B:G.426, B:G.428, B:S.429, B:S.429, B:G.458, B:A.459 Water bridges: B:D.427, B:N.454, A:H.69 TZD.23: 26 residues within 4Å: Chain C: E.374, S.375, T.376, S.377, G.400, G.401, L.402, G.426, D.427, G.428, S.429, Y.432, N.454, T.456, Y.457, G.458, A.459, L.460 Chain D: N.22, P.23, G.24, E.46, H.69, N.76 Ligands: CA.24, EDO.28 17 PLIP interactions: 16 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:Y.432, C:L.460 Hydrogen bonds: C:T.376, C:S.377, C:G.400, C:L.402, C:G.426, C:G.428, C:S.429, C:S.429, C:Y.432, C:N.454, C:G.458, C:A.459 Water bridges: C:D.427, C:N.454, D:H.69 TZD.34: 26 residues within 4Å: Chain C: N.22, P.23, G.24, E.46, H.69, N.76 Chain D: E.374, S.375, T.376, S.377, G.400, G.401, L.402, G.426, D.427, G.428, S.429, Y.432, N.454, T.456, Y.457, G.458, A.459, L.460 Ligands: CA.35, EDO.39 17 PLIP interactions: 16 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:Y.432, D:L.460 Hydrogen bonds: D:T.376, D:S.377, D:G.400, D:L.402, D:G.426, D:G.428, D:S.429, D:S.429, D:Y.432, D:N.454, D:G.458, D:A.459 Water bridges: D:D.427, D:N.454, C:H.69

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: D.427, N.454, T.456 Ligands: TZD.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.427, A:T.456, H2O.1 CA.13: 4 residues within 4Å: Chain B: D.427, N.454, T.456 Ligands: TZD.12 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.427, B:T.456, H2O.18 CA.24: 4 residues within 4Å: Chain C: D.427, N.454, T.456 Ligands: TZD.23 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.427, C:T.456, H2O.34 CA.35: 4 residues within 4Å: Chain D: D.427, N.454, T.456 Ligands: TZD.34 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.427, D:T.456, H2O.51

36 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 8 residues within 4Å: Chain A: W.85, N.86, H.88, P.275, D.300, E.303, R.306 Chain B: E.106 Ligand excluded by PLIP EDO.4: 7 residues within 4Å: Chain A: A.148, P.149, V.182, C.299, V.314, A.315 Ligands: EDO.26 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain A: N.214, A.215, N.216, A.217, D.218 Ligand excluded by PLIP EDO.6: 10 residues within 4Å: Chain A: A.47, G.79, A.80, N.83, G.401, L.402, G.403 Chain B: A.72, N.76 Ligands: TZD.1 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain A: G.255, I.256, A.257, A.258 Ligand excluded by PLIP EDO.8: 6 residues within 4Å: Chain A: Q.413, P.417, E.418, R.419, Q.420, P.446 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: K.495, Q.501, G.504, S.505 Ligand excluded by PLIP EDO.10: 6 residues within 4Å: Chain A: R.119, W.124, S.125, Y.126, R.140 Chain D: V.112 Ligand excluded by PLIP EDO.11: 2 residues within 4Å: Chain A: A.1, D.165 Ligand excluded by PLIP EDO.14: 8 residues within 4Å: Chain A: E.106 Chain B: W.85, N.86, H.88, P.275, D.300, E.303, R.306 Ligand excluded by PLIP EDO.15: 7 residues within 4Å: Chain B: A.148, P.149, V.182, C.299, V.314, A.315 Ligands: EDO.37 Ligand excluded by PLIP EDO.16: 5 residues within 4Å: Chain B: N.214, A.215, N.216, A.217, D.218 Ligand excluded by PLIP EDO.17: 10 residues within 4Å: Chain A: A.72, N.76 Chain B: A.47, G.79, A.80, N.83, G.401, L.402, G.403 Ligands: TZD.12 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain B: G.255, I.256, A.257, A.258 Ligand excluded by PLIP EDO.19: 6 residues within 4Å: Chain B: Q.413, P.417, E.418, R.419, Q.420, P.446 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain B: K.495, Q.501, G.504, S.505 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain B: R.119, W.124, S.125, Y.126, R.140 Chain C: V.112 Ligand excluded by PLIP EDO.22: 2 residues within 4Å: Chain B: A.1, D.165 Ligand excluded by PLIP EDO.25: 8 residues within 4Å: Chain C: W.85, N.86, H.88, P.275, D.300, E.303, R.306 Chain D: E.106 Ligand excluded by PLIP EDO.26: 7 residues within 4Å: Chain C: A.148, P.149, V.182, C.299, V.314, A.315 Ligands: EDO.4 Ligand excluded by PLIP EDO.27: 5 residues within 4Å: Chain C: N.214, A.215, N.216, A.217, D.218 Ligand excluded by PLIP EDO.28: 10 residues within 4Å: Chain C: A.47, G.79, A.80, N.83, G.401, L.402, G.403 Chain D: A.72, N.76 Ligands: TZD.23 Ligand excluded by PLIP EDO.29: 4 residues within 4Å: Chain C: G.255, I.256, A.257, A.258 Ligand excluded by PLIP EDO.30: 6 residues within 4Å: Chain C: Q.413, P.417, E.418, R.419, Q.420, P.446 Ligand excluded by PLIP EDO.31: 4 residues within 4Å: Chain C: K.495, Q.501, G.504, S.505 Ligand excluded by PLIP EDO.32: 6 residues within 4Å: Chain B: V.112 Chain C: R.119, W.124, S.125, Y.126, R.140 Ligand excluded by PLIP EDO.33: 2 residues within 4Å: Chain C: A.1, D.165 Ligand excluded by PLIP EDO.36: 8 residues within 4Å: Chain C: E.106 Chain D: W.85, N.86, H.88, P.275, D.300, E.303, R.306 Ligand excluded by PLIP EDO.37: 7 residues within 4Å: Chain D: A.148, P.149, V.182, C.299, V.314, A.315 Ligands: EDO.15 Ligand excluded by PLIP EDO.38: 5 residues within 4Å: Chain D: N.214, A.215, N.216, A.217, D.218 Ligand excluded by PLIP EDO.39: 10 residues within 4Å: Chain C: A.72, N.76 Chain D: A.47, G.79, A.80, N.83, G.401, L.402, G.403 Ligands: TZD.34 Ligand excluded by PLIP EDO.40: 4 residues within 4Å: Chain D: G.255, I.256, A.257, A.258 Ligand excluded by PLIP EDO.41: 6 residues within 4Å: Chain D: Q.413, P.417, E.418, R.419, Q.420, P.446 Ligand excluded by PLIP EDO.42: 4 residues within 4Å: Chain D: K.495, Q.501, G.504, S.505 Ligand excluded by PLIP EDO.43: 6 residues within 4Å: Chain A: V.112 Chain D: R.119, W.124, S.125, Y.126, R.140 Ligand excluded by PLIP EDO.44: 2 residues within 4Å: Chain D: A.1, D.165 Ligand excluded by PLIP

Links

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Citation

Brodkin, H.R. et al., Crystal Structure of the His281Thr mutant of Benzoylformate Decarboxylase from Pseudomonas putida. To be Published

Release Date

2013-05-08

Peptides

Benzoylformate decarboxylase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Benzoylformate decarboxylase