SMTL ID : 5tma.1

Zymomonas mobilis pyruvate decarboxylase mutant PDC-2.3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.67 Å

Oligo State

homo-tetramer

Ligands

4 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.1: 24 residues within 4Å: Chain A: T.388, G.389, D.390, G.413, H.414, I.415, G.439, D.440, G.441, S.442, L.445, N.467, G.469, Y.470, T.471, I.472, E.473 Chain C: A.25, G.26, E.50, T.72, V.75, H.114 Ligands: MG.2 24 PLIP interactions: 23 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:I.415, A:I.415, A:L.445, A:Y.470, A:Y.470, A:I.472, A:E.473 Hydrogen bonds: A:D.390, A:G.413, A:I.415, A:G.439, A:D.440, A:G.441, A:S.442, A:N.467, A:T.471, A:T.471, A:I.472 Water bridges: A:S.391, A:D.440, A:D.440, A:S.442, A:S.442, C:E.50 TPP.18: 24 residues within 4Å: Chain B: T.388, G.389, D.390, G.413, H.414, I.415, G.439, D.440, G.441, S.442, L.445, N.467, G.469, Y.470, T.471, I.472, E.473 Chain D: A.25, G.26, E.50, T.72, V.75, H.114 Ligands: MG.19 21 PLIP interactions: 20 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:I.415, B:I.415, B:L.445, B:Y.470, B:Y.470, B:I.472, D:V.75 Hydrogen bonds: B:D.390, B:G.413, B:I.415, B:G.439, B:G.441, B:S.442, B:N.467, B:T.471, B:I.472 Water bridges: B:S.391, B:D.440, B:S.442, B:S.442, B:N.467 TPP.39: 24 residues within 4Å: Chain A: A.25, G.26, E.50, T.72, V.75, H.114 Chain C: T.388, G.389, D.390, G.413, H.414, I.415, G.439, D.440, G.441, S.442, L.445, N.467, G.469, Y.470, T.471, I.472, E.473 Ligands: MG.40 21 PLIP interactions: 21 interactions with chain C Hydrophobic interactions: C:I.415, C:I.415, C:L.445, C:Y.470, C:Y.470, C:I.472, C:E.473 Hydrogen bonds: C:D.390, C:G.413, C:I.415, C:G.439, C:G.441, C:S.442, C:N.467, C:T.471, C:I.472 Water bridges: C:S.391, C:D.440, C:D.440, C:S.442, C:S.442 TPP.56: 24 residues within 4Å: Chain B: A.25, G.26, E.50, T.72, V.75, H.114 Chain D: T.388, G.389, D.390, G.413, H.414, I.415, G.439, D.440, G.441, S.442, L.445, N.467, G.469, Y.470, T.471, I.472, E.473 Ligands: MG.57 23 PLIP interactions: 21 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: D:I.415, D:I.415, D:L.445, D:Y.470, D:Y.470, D:I.472, B:V.75 Hydrogen bonds: D:D.390, D:G.413, D:I.415, D:G.439, D:G.441, D:S.442, D:N.467, D:T.471, D:T.471, D:I.472 Water bridges: D:S.391, D:D.440, D:S.442, D:S.442, D:N.467, B:E.50

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.440, N.467, G.469 Ligands: TPP.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.440, A:G.469, H2O.11 MG.19: 4 residues within 4Å: Chain B: D.440, N.467, G.469 Ligands: TPP.18 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.440, B:G.469, H2O.30 MG.40: 4 residues within 4Å: Chain C: D.440, N.467, G.469 Ligands: TPP.39 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.440, C:G.469, H2O.49 MG.57: 4 residues within 4Å: Chain D: D.440, N.467, G.469 Ligands: TPP.56 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.440, D:G.469, H2O.69

32 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 4 residues within 4Å: Chain A: I.484, K.485, N.486 Chain C: S.504 Ligand excluded by PLIP SO4.4: 4 residues within 4Å: Chain A: D.234, G.237, H.256, K.337 Ligand excluded by PLIP SO4.5: 5 residues within 4Å: Chain A: E.308, P.309, R.310, S.311, R.318 Ligand excluded by PLIP SO4.6: 8 residues within 4Å: Chain A: H.106, A.107, D.120, Y.121, H.122 Chain D: H.122, Y.139 Ligands: SO4.61 Ligand excluded by PLIP SO4.7: 3 residues within 4Å: Chain A: K.153, R.157 Chain B: R.310 Ligand excluded by PLIP SO4.8: 4 residues within 4Å: Chain A: T.379, N.381, T.382, R.433 Ligand excluded by PLIP SO4.20: 3 residues within 4Å: Chain B: Q.15, P.180, A.181 Ligand excluded by PLIP SO4.21: 5 residues within 4Å: Chain B: S.504 Chain D: I.484, K.485, N.486 Ligands: EDO.37 Ligand excluded by PLIP SO4.22: 4 residues within 4Å: Chain B: D.234, G.237, H.256, K.337 Ligand excluded by PLIP SO4.23: 7 residues within 4Å: Chain B: H.106, A.107, T.119, D.120, Y.121, H.122 Ligands: SO4.44 Ligand excluded by PLIP SO4.24: 4 residues within 4Å: Chain A: E.188, R.310 Chain B: K.153, R.157 Ligand excluded by PLIP SO4.25: 4 residues within 4Å: Chain B: E.308, P.309, R.310, S.311 Ligand excluded by PLIP SO4.26: 4 residues within 4Å: Chain B: T.379, N.381, T.382, R.433 Ligand excluded by PLIP SO4.27: 2 residues within 4Å: Chain B: E.136, H.150 Ligand excluded by PLIP SO4.28: 7 residues within 4Å: Chain B: T.260, V.265, Y.267, F.393, Q.396, R.397, E.547 Ligand excluded by PLIP SO4.29: 4 residues within 4Å: Chain B: P.268, G.269, K.272, A.350 Ligand excluded by PLIP SO4.41: 4 residues within 4Å: Chain A: S.504 Chain C: I.484, K.485, N.486 Ligand excluded by PLIP SO4.42: 4 residues within 4Å: Chain C: D.234, G.237, H.256, K.337 Ligand excluded by PLIP SO4.43: 5 residues within 4Å: Chain C: E.308, P.309, R.310, S.311, R.318 Ligand excluded by PLIP SO4.44: 8 residues within 4Å: Chain B: H.122, Y.139 Chain C: H.106, A.107, D.120, Y.121, H.122 Ligands: SO4.23 Ligand excluded by PLIP SO4.45: 3 residues within 4Å: Chain C: K.153, R.157 Chain D: R.310 Ligand excluded by PLIP SO4.46: 4 residues within 4Å: Chain C: T.379, N.381, T.382, R.433 Ligand excluded by PLIP SO4.58: 3 residues within 4Å: Chain D: Q.15, P.180, A.181 Ligand excluded by PLIP SO4.59: 5 residues within 4Å: Chain B: I.484, K.485, N.486 Chain D: S.504 Ligands: EDO.75 Ligand excluded by PLIP SO4.60: 4 residues within 4Å: Chain D: D.234, G.237, H.256, K.337 Ligand excluded by PLIP SO4.61: 7 residues within 4Å: Chain D: H.106, A.107, T.119, D.120, Y.121, H.122 Ligands: SO4.6 Ligand excluded by PLIP SO4.62: 4 residues within 4Å: Chain C: E.188, R.310 Chain D: K.153, R.157 Ligand excluded by PLIP SO4.63: 4 residues within 4Å: Chain D: E.308, P.309, R.310, S.311 Ligand excluded by PLIP SO4.64: 4 residues within 4Å: Chain D: T.379, N.381, T.382, R.433 Ligand excluded by PLIP SO4.65: 2 residues within 4Å: Chain D: E.136, H.150 Ligand excluded by PLIP SO4.66: 7 residues within 4Å: Chain D: T.260, V.265, Y.267, F.393, Q.396, R.397, E.547 Ligand excluded by PLIP SO4.67: 4 residues within 4Å: Chain D: P.268, G.269, K.272, A.350 Ligand excluded by PLIP

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

EDO.9: 4 residues within 4Å: Chain A: E.192, L.195, N.196, R.330 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: I.16, K.64, G.65, A.66, L.156 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain A: E.252, Y.257, I.258, G.259, Y.267, K.399 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain A: R.157, K.159, K.219, A.222, P.309, R.310 Ligand excluded by PLIP EDO.13: 7 residues within 4Å: Chain A: K.153, L.156, R.157, L.184, F.185, N.186, D.187 Ligand excluded by PLIP EDO.14: 3 residues within 4Å: Chain A: S.190, D.191, E.192 Ligand excluded by PLIP EDO.15: 6 residues within 4Å: Chain A: R.157, D.187, E.188 Chain B: R.157, D.187, E.188 Ligand excluded by PLIP EDO.16: 1 residues within 4Å: Chain C: R.455 Ligand excluded by PLIP EDO.17: 8 residues within 4Å: Chain A: F.205, P.301, K.302, L.304, V.305, V.314, N.315, G.316 Ligand excluded by PLIP EDO.30: 5 residues within 4Å: Chain B: E.252, Y.257, I.258, Y.267, K.399 Ligand excluded by PLIP EDO.31: 6 residues within 4Å: Chain B: S.248, P.251, P.401, N.402, G.403, A.404 Ligand excluded by PLIP EDO.32: 8 residues within 4Å: Chain B: F.205, P.301, K.302, L.304, V.305, V.314, N.315, G.316 Ligand excluded by PLIP EDO.33: 5 residues within 4Å: Chain B: E.158, K.159, A.222, P.309, R.310 Ligand excluded by PLIP EDO.34: 6 residues within 4Å: Chain B: P.141, E.142, P.145, P.174, C.175, A.176 Ligand excluded by PLIP EDO.35: 1 residues within 4Å: Chain B: N.402 Ligand excluded by PLIP EDO.36: 6 residues within 4Å: Chain B: L.116, G.117, K.118 Chain D: Y.88, K.160, K.219 Ligand excluded by PLIP EDO.37: 6 residues within 4Å: Chain B: R.455, K.457, S.504, G.505 Chain D: K.485 Ligands: SO4.21 Ligand excluded by PLIP EDO.38: 5 residues within 4Å: Chain B: M.1, D.38, N.39, K.40, N.41 Ligand excluded by PLIP EDO.47: 4 residues within 4Å: Chain C: E.192, L.195, N.196, R.330 Ligand excluded by PLIP EDO.48: 5 residues within 4Å: Chain C: I.16, K.64, G.65, A.66, L.156 Ligand excluded by PLIP EDO.49: 6 residues within 4Å: Chain C: E.252, Y.257, I.258, G.259, Y.267, K.399 Ligand excluded by PLIP EDO.50: 6 residues within 4Å: Chain C: R.157, K.159, K.219, A.222, P.309, R.310 Ligand excluded by PLIP EDO.51: 7 residues within 4Å: Chain C: K.153, L.156, R.157, L.184, F.185, N.186, D.187 Ligand excluded by PLIP EDO.52: 3 residues within 4Å: Chain C: S.190, D.191, E.192 Ligand excluded by PLIP EDO.53: 6 residues within 4Å: Chain C: R.157, D.187, E.188 Chain D: R.157, D.187, E.188 Ligand excluded by PLIP EDO.54: 1 residues within 4Å: Chain A: R.455 Ligand excluded by PLIP EDO.55: 8 residues within 4Å: Chain C: F.205, P.301, K.302, L.304, V.305, V.314, N.315, G.316 Ligand excluded by PLIP EDO.68: 5 residues within 4Å: Chain D: E.252, Y.257, I.258, Y.267, K.399 Ligand excluded by PLIP EDO.69: 6 residues within 4Å: Chain D: S.248, P.251, P.401, N.402, G.403, A.404 Ligand excluded by PLIP EDO.70: 8 residues within 4Å: Chain D: F.205, P.301, K.302, L.304, V.305, V.314, N.315, G.316 Ligand excluded by PLIP EDO.71: 5 residues within 4Å: Chain D: E.158, K.159, A.222, P.309, R.310 Ligand excluded by PLIP EDO.72: 6 residues within 4Å: Chain D: P.141, E.142, P.145, P.174, C.175, A.176 Ligand excluded by PLIP EDO.73: 1 residues within 4Å: Chain D: N.402 Ligand excluded by PLIP EDO.74: 6 residues within 4Å: Chain B: Y.88, K.160, K.219 Chain D: L.116, G.117, K.118 Ligand excluded by PLIP EDO.75: 6 residues within 4Å: Chain B: K.485 Chain D: R.455, K.457, S.504, G.505 Ligands: SO4.59 Ligand excluded by PLIP EDO.76: 5 residues within 4Å: Chain D: M.1, D.38, N.39, K.40, N.41 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sammond, D.W. et al., An iterative computational design approach to increase the thermal endurance of a mesophilic enzyme. Biotechnol Biofuels (2018)

Release Date

2017-10-18

Peptides

Pyruvate decarboxylase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Pyruvate decarboxylase