SMTL ID : 5dei.1

BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-tetramer

Ligands

4 x BCT: BICARBONATE ION(Non-functional Binders)

BCT.1: 8 residues within 4Å: Chain A: G.24, S.25, H.69, L.109 Chain C: H.280, L.460, F.463 Ligands: TPP.17 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.280 Water bridges: C:G.400 BCT.8: 8 residues within 4Å: Chain B: G.24, S.25, H.69, L.109 Chain D: H.280, L.460, F.463 Ligands: TPP.20 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.25, B:H.69 BCT.16: 8 residues within 4Å: Chain A: H.280, L.460, F.463 Chain C: G.24, S.25, H.69, L.109 Ligands: TPP.2 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.25, C:S.25, C:H.69 BCT.19: 8 residues within 4Å: Chain B: H.280, L.460, F.463 Chain D: G.24, S.25, H.69, L.109 Ligands: TPP.9 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:H.69

4 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.2: 31 residues within 4Å: Chain A: E.374, S.375, T.376, S.377, T.378, 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, S.25, E.46, H.69, A.72, G.73, N.76, L.109 Ligands: CA.7, BCT.16 23 PLIP interactions: 22 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:L.402, A:Y.432, A:L.460 Hydrogen bonds: A:T.376, A:T.376, A:S.377, A:S.377, A:G.400, A:L.402, A:G.426, A:G.426, A:G.428, A:S.429, A:S.429, A:Y.432, A:N.454, A:G.458, A:A.459 Water bridges: A:S.375, A:S.377, A:D.427, A:N.454, C:H.69 TPP.9: 31 residues within 4Å: Chain B: E.374, S.375, T.376, S.377, T.378, 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, S.25, E.46, H.69, A.72, G.73, N.76, L.109 Ligands: CA.14, BCT.19 21 PLIP interactions: 20 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:Y.432, B:L.460 Hydrogen bonds: B:T.376, B:T.376, B:T.376, B:S.377, B:S.377, B:G.400, B:L.402, B:G.426, B:G.428, B:S.429, B:S.429, B:Y.432, B:N.454, B:T.456, B:G.458, B:A.459 Water bridges: B:D.427, B:N.454, D:H.69 TPP.17: 30 residues within 4Å: Chain A: N.22, P.23, G.24, S.25, E.46, H.69, A.72, G.73, N.76 Chain C: E.374, S.375, T.376, S.377, T.378, 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: BCT.1, CA.18 21 PLIP interactions: 20 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:Y.432, C:L.460 Hydrogen bonds: C:T.376, C:T.376, C:T.376, C:S.377, C:S.377, C:G.400, C:L.402, C:G.426, 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, A:H.69 TPP.20: 31 residues within 4Å: Chain B: N.22, P.23, G.24, S.25, E.46, H.69, A.72, G.73, N.76, L.109 Chain D: E.374, S.375, T.376, S.377, T.378, 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: BCT.8, CA.22 21 PLIP interactions: 20 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:Y.432, D:L.460 Hydrogen bonds: D:T.376, D:T.376, D:T.376, D:S.377, 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:T.456, D:G.458, D:A.459 Water bridges: D:D.427, D:N.454, B:H.69

8 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 7 residues within 4Å: Chain A: N.116, L.117, R.119 Chain C: M.78, N.116, L.117, R.119 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain C Metal complexes: A:N.116, A:L.117, A:R.119, C:N.116, C:L.117, C:R.119 MG.4: 2 residues within 4Å: Chain A: L.494, K.495 No protein-ligand interaction detected (PLIP) MG.5: 4 residues within 4Å: Chain A: R.183, A.323 Chain D: N.185, D.186 No protein-ligand interaction detected (PLIP) MG.10: 7 residues within 4Å: Chain B: N.116, L.117, R.119 Chain D: M.78, N.116, L.117, R.119 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain B Metal complexes: D:N.116, D:L.117, D:R.119, B:N.116, B:L.117, B:R.119 MG.11: 3 residues within 4Å: Chain B: R.183 Chain C: N.185, D.186 No protein-ligand interaction detected (PLIP) MG.12: 2 residues within 4Å: Chain B: L.494, K.495 No protein-ligand interaction detected (PLIP) MG.13: 1 residues within 4Å: Chain B: Q.492 No protein-ligand interaction detected (PLIP) MG.21: 2 residues within 4Å: Chain D: L.494, K.495 No protein-ligand interaction detected (PLIP)

6 x CA: CALCIUM ION(Non-covalent)

CA.6: 3 residues within 4Å: Chain A: N.185, D.186 Chain D: R.183 No protein-ligand interaction detected (PLIP) CA.7: 6 residues within 4Å: Chain A: D.427, G.428, N.454, T.456, G.458 Ligands: TPP.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.427, A:T.456, H2O.2 CA.14: 6 residues within 4Å: Chain B: D.427, G.428, N.454, T.456, G.458 Ligands: TPP.9 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.427, B:T.456, H2O.26 CA.15: 3 residues within 4Å: Chain B: N.185, D.186 Chain C: R.183 No protein-ligand interaction detected (PLIP) CA.18: 6 residues within 4Å: Chain C: D.427, G.428, N.454, T.456, G.458 Ligands: TPP.17 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.427, C:T.456, H2O.49 CA.22: 6 residues within 4Å: Chain D: D.427, G.428, N.454, T.456, G.458 Ligands: TPP.20 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.427, D:T.456, H2O.72

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bera, A.K. et al., BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA. to be published

Release Date

2015-09-16

Peptides

Benzoylformate decarboxylase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Benzoylformate decarboxylase