SMTL ID : 4k9m.1

Crystal Structure of the His281Asn mutant of Benzoylformate Decarboxylase from Pseudomonas putida

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.15 Å

Oligo State

homo-tetramer

Ligands

4 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.1: 25 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 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:L.402, A:Y.432, A:L.460 Hydrogen bonds: A:S.375, A:T.376, A:S.377, A:G.400, A:L.402, A:G.426, A:G.428, A:S.429, A:N.454, A:G.458, A:A.459 Water bridges: A:D.427, A:D.427, A:S.429, A:S.429 TPP.6: 25 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.7 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:L.402, B:Y.432, B:L.460 Hydrogen bonds: B:S.375, B:T.376, B:S.377, B:G.400, B:L.402, B:G.426, B:G.428, B:S.429, B:N.454, B:G.458, B:A.459 Water bridges: B:D.427, B:D.427, B:S.429, B:S.429 TPP.11: 25 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.12 20 PLIP interactions: 20 interactions with chain C Hydrophobic interactions: C:L.402, C:Y.432, C:L.460 Hydrogen bonds: C:S.375, C:T.376, C:S.377, C:G.400, C:L.402, C:G.426, C:G.428, C:S.429, C:Y.432, C:N.454, C:G.458, C:A.459 Water bridges: C:T.376, C:D.427, C:D.427, C:S.429, C:S.429 TPP.16: 25 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.17 20 PLIP interactions: 20 interactions with chain D Hydrophobic interactions: D:L.402, D:Y.432, D:L.460 Hydrogen bonds: D:S.375, D:T.376, D:S.377, D:G.400, D:L.402, D:G.426, D:G.428, D:S.429, D:Y.432, D:N.454, D:G.458, D:A.459 Water bridges: D:T.376, D:D.427, D:D.427, D:S.429, D:S.429

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: D.427, N.454, T.456 Ligands: TPP.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.427, A:T.456, H2O.2 CA.7: 4 residues within 4Å: Chain B: D.427, N.454, T.456 Ligands: TPP.6 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.427, B:T.456, H2O.26 CA.12: 4 residues within 4Å: Chain C: D.427, N.454, T.456 Ligands: TPP.11 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.427, C:T.456, H2O.51 CA.17: 4 residues within 4Å: Chain D: D.427, N.454, T.456 Ligands: TPP.16 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.427, D:T.456, H2O.75

12 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain A: L.10, Q.14, S.139, H.143, L.173, R.176 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:S.139, A:H.143, A:L.173 MG.4: 7 residues within 4Å: Chain A: N.116, L.117, R.119 Chain B: N.116, L.117, R.119 Ligands: MG.9 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Metal complexes: B:N.116, B:L.117, B:R.119, A:N.116, A:L.117, A:R.119 MG.5: 3 residues within 4Å: Chain A: N.185, D.186 Chain C: R.183 No protein-ligand interaction detected (PLIP) MG.8: 6 residues within 4Å: Chain B: L.10, Q.14, S.139, H.143, L.173, R.176 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:S.139, B:H.143, B:L.173 MG.9: 7 residues within 4Å: Chain A: N.116, L.117, R.119 Chain B: N.116, L.117, R.119 Ligands: MG.4 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Metal complexes: B:N.116, B:L.117, B:R.119, A:N.116, A:L.117, A:R.119 MG.10: 3 residues within 4Å: Chain B: N.185, D.186 Chain D: R.183 No protein-ligand interaction detected (PLIP) MG.13: 6 residues within 4Å: Chain C: L.10, Q.14, S.139, H.143, L.173, R.176 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:S.139, C:H.143, C:L.173 MG.14: 7 residues within 4Å: Chain C: N.116, L.117, R.119 Chain D: N.116, L.117, R.119 Ligands: MG.19 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain C Metal complexes: D:N.116, D:L.117, D:R.119, C:N.116, C:L.117, C:R.119 MG.15: 3 residues within 4Å: Chain A: R.183 Chain C: N.185, D.186 No protein-ligand interaction detected (PLIP) MG.18: 6 residues within 4Å: Chain D: L.10, Q.14, S.139, H.143, L.173, R.176 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:S.139, D:H.143, D:L.173 MG.19: 7 residues within 4Å: Chain C: N.116, L.117, R.119 Chain D: N.116, L.117, R.119 Ligands: MG.14 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain C Metal complexes: D:N.116, D:L.117, D:R.119, C:N.116, C:L.117, C:R.119 MG.20: 3 residues within 4Å: Chain B: R.183 Chain D: N.185, D.186 No protein-ligand interaction detected (PLIP)

Links

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Citation

Brodkin, H.R. et al., Crystal Structure of the His281Asn 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