SMTL ID : 4juc.1

Crystal Structure of the Ser26Met mutant of Benzoylformate Decarboxylase from Pseudomonas putida

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: D.428, N.455, T.457 Ligands: TPP.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.428, A:T.457 CA.5: 4 residues within 4Å: Chain B: D.428, N.455, T.457 Ligands: TPP.6 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.428, B:T.457 CA.9: 5 residues within 4Å: Chain C: D.428, N.455, T.457, G.459 Ligands: TPP.10 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.428, C:T.457 CA.13: 4 residues within 4Å: Chain D: D.428, N.455, T.457 Ligands: TPP.14 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.428, D:T.457

4 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.2: 25 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 C: N.23, P.24, G.25, E.47, H.70, N.77 Ligands: CA.1 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:L.403, A:Y.433, A:Y.458, A:L.461 Hydrogen bonds: A:T.377, A:T.377, A:T.377, A:S.378, A:G.401, A:L.403, A:D.428, A:D.428, A:G.429, A:S.430, A:Y.433, A:N.455, A:G.459, A:A.460 TPP.6: 24 residues within 4Å: Chain B: E.375, S.376, T.377, S.378, G.401, 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.5 18 PLIP interactions: 17 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:L.403, B:L.403, B:Y.433, B:Y.458, B:L.461 Hydrogen bonds: B:T.377, B:T.377, B:T.377, B:S.378, B:G.401, B:L.403, B:G.427, B:G.429, B:S.430, B:N.455, B:G.459, B:A.460 Water bridges: D:E.47 TPP.10: 24 residues within 4Å: Chain A: N.23, P.24, G.25, E.47, H.70, N.77 Chain C: E.375, S.376, T.377, S.378, G.401, 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: CA.9 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:Y.433, C:L.461 Hydrogen bonds: C:T.377, C:T.377, C:S.378, C:G.401, C:L.403, C:G.429, C:S.430, C:Y.433, C:N.455, C:N.455, C:G.459, C:A.460 TPP.14: 24 residues within 4Å: Chain B: N.23, P.24, G.25, E.47, H.70, N.77 Chain D: E.375, S.376, T.377, S.378, G.401, 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: CA.13 15 PLIP interactions: 14 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:Y.433, D:Y.458, D:L.461 Hydrogen bonds: D:S.376, 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:G.459, D:A.460 Water bridges: B:H.70

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: R.101, E.128, P.129, A.130 Chain B: R.101, E.128, P.129, A.130 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.101, A:P.129, B:R.101, B:E.128, B:P.129 Water bridges: A:A.130 GOL.4: 7 residues within 4Å: Chain A: A.133, E.134, H.137, D.168 Chain B: A.102, G.105 Chain D: Y.288 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.131, A:S.131, A:H.137, A:D.168 Water bridges: B:G.105, B:V.106 GOL.7: 1 residues within 4Å: Chain B: D.364 2 PLIP interactions: 2 interactions with chain B Water bridges: B:E.342, B:E.342 GOL.8: 6 residues within 4Å: Chain B: I.192, L.193, A.196, R.294, I.296, D.312 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.294, B:R.294, B:D.312 Water bridges: B:I.192, B:L.193, B:A.196 GOL.11: 7 residues within 4Å: Chain C: E.128, P.129, A.130 Chain D: R.101, E.128, P.129, A.130 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:R.101, C:P.129, D:R.101, D:P.129 Water bridges: C:E.128, C:E.128 GOL.12: 6 residues within 4Å: Chain C: Q.421, P.447, A.510, L.511, S.512, A.513 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.512

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brodkin, H.R. et al., Crystal Structure of the Ser26Met 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
A

B
B

C
C

D
D

Benzoylformate decarboxylase