SMTL ID : 4juf.1

Crystal Structure of His281Ala mutant of Benzoylformate Decarboxylase from Pseudomonas putida

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-tetramer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain A: N.116, L.117, R.119 Chain C: N.116, L.117, R.119 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain C Metal complexes: A:L.117, A:R.119, C:N.116, C:L.117, C:R.119 MG.5: 6 residues within 4Å: Chain B: N.116, L.117, R.119 Chain D: N.116, L.117, R.119 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain D Metal complexes: B:N.116, B:L.117, B:R.119, D:N.116, D:L.117, D:R.119

5 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: D.427, N.454, T.456 Ligands: TPP.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.427, A:T.456, H2O.1 CA.6: 4 residues within 4Å: Chain B: D.427, N.454, T.456 Ligands: TPP.7 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.427, B:T.456, H2O.13 CA.8: 2 residues within 4Å: Chain B: Q.420, L.510 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:L.510, H2O.18, H2O.20 CA.9: 4 residues within 4Å: Chain C: D.427, N.454, T.456 Ligands: TPP.10 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.427, C:T.456, H2O.22 CA.12: 4 residues within 4Å: Chain D: D.427, N.454, T.456 Ligands: TPP.13 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.427, D:T.456, H2O.33

4 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.3: 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 C: N.22, P.23, G.24, E.46, H.69, N.76 Ligands: CA.2 18 PLIP interactions: 17 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:Y.432, A:Y.457, 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:Y.432, A:N.454, A:G.458, A:A.459 Water bridges: A:N.454, A:N.454, C:E.46 TPP.7: 25 residues within 4Å: 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 Chain D: N.22, P.23, G.24, E.46, H.69, N.76 Ligands: CA.6 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:Y.432, B:L.460 Hydrogen bonds: B:S.375, B:T.376, B:T.376, B:S.377, B:S.377, B:G.400, B:L.402, B:G.428, B:S.429, B:N.454, B:G.458, B:A.459 Water bridges: B:D.427, B:D.427 TPP.10: 25 residues within 4Å: Chain A: N.22, P.23, G.24, E.46, H.69, N.76 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 Ligands: CA.9 19 PLIP interactions: 18 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:Y.432, C:L.460 Hydrogen bonds: C:S.375, C:T.376, C:T.376, C:S.377, 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:D.427, C:N.454, A:H.69 TPP.13: 25 residues within 4Å: Chain B: 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.12 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:Y.432, D:L.460 Hydrogen bonds: D:S.375, D:T.376, D:T.376, D:S.377, D:S.377, D:G.400, D:L.402, D:G.428, D:S.429, D:N.454, D:G.458, D:A.459 Water bridges: D:N.454, D:N.454

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 8 residues within 4Å: Chain A: R.100, E.127, P.128, A.129 Chain D: R.100, E.127, P.128, A.129 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:R.100, D:E.127, D:E.127, A:R.100 GOL.11: 8 residues within 4Å: Chain B: R.100, E.127, P.128, A.129 Chain C: R.100, E.127, P.128, A.129 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:R.100, B:E.127, B:E.127, C:R.100, C:P.128

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brodkin, H.R. et al., Crystal Structure of His281Ala mutant of Benzoylformate Decarboxylase from Pseudomonas putida. To be Published

Release Date

2013-05-01

Peptides

Benzoylformate decarboxylase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Benzoylformate decarboxylase