SMTL ID : 5dgt.1

BENZOYLFORMATE DECARBOXYLASE H70A MUTANT at pH 8.5 FROM PSEUDOMONAS PUTIDA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.08 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 9 residues within 4Å: Chain A: M.78, N.116, L.117, R.119 Chain B: M.78, N.116, L.117, R.119 Ligands: MG.6 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.6: 9 residues within 4Å: Chain A: M.78, N.116, L.117, R.119 Chain B: M.78, N.116, L.117, R.119 Ligands: MG.1 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.11: 9 residues within 4Å: Chain C: M.78, N.116, L.117, R.119 Chain D: M.78, N.116, L.117, R.119 Ligands: MG.16 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.16: 9 residues within 4Å: Chain C: M.78, N.116, L.117, R.119 Chain D: M.78, N.116, L.117, R.119 Ligands: MG.11 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain D Metal complexes: C:N.116, C:L.117, C:R.119, D:N.116, D:L.117, D:R.119

12 x CA: CALCIUM ION(Non-covalent)

CA.2: 7 residues within 4Å: Chain A: D.427, G.428, N.454, T.456, Y.457, G.458 Ligands: TZD.5 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.427, A:T.456, H2O.3 CA.3: 2 residues within 4Å: Chain A: N.362, D.363 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.363, H2O.8, H2O.20, H2O.20, H2O.21 CA.4: 2 residues within 4Å: Chain A: A.415, P.417 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:A.415, H2O.10, H2O.13, H2O.20, H2O.21 CA.7: 7 residues within 4Å: Chain B: D.427, G.428, N.454, T.456, Y.457, G.458 Ligands: TZD.10 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.427, B:T.456, H2O.31 CA.8: 2 residues within 4Å: Chain B: N.362, D.363 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.363, H2O.36, H2O.48, H2O.49, H2O.50 CA.9: 2 residues within 4Å: Chain B: A.415, P.417 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:A.415, H2O.38, H2O.41, H2O.48, H2O.49 CA.12: 7 residues within 4Å: Chain C: D.427, G.428, N.454, T.456, Y.457, G.458 Ligands: TZD.15 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.427, C:T.456, H2O.60 CA.13: 2 residues within 4Å: Chain C: N.362, D.363 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:D.363, H2O.64, H2O.77, H2O.77, H2O.78 CA.14: 2 residues within 4Å: Chain C: A.415, P.417 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:A.415, H2O.66, H2O.69, H2O.76, H2O.77 CA.17: 7 residues within 4Å: Chain D: D.427, G.428, N.454, T.456, Y.457, G.458 Ligands: TZD.20 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.427, D:T.456, H2O.88 CA.18: 2 residues within 4Å: Chain D: N.362, D.363 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:D.363, H2O.92, H2O.105, H2O.105, H2O.106 CA.19: 2 residues within 4Å: Chain D: A.415, P.417 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:A.415, H2O.94, H2O.97, H2O.104, H2O.105

4 x TZD: 2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL-2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYL TRIHYDROGEN DIPHOSPHATE(Non-covalent)

TZD.5: 30 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 B: N.22, P.23, G.24, S.25, E.46, A.69, A.72, G.73, N.76, L.109 Ligands: CA.2 23 PLIP interactions: 21 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.432, A:L.460, B:A.69 Hydrogen bonds: A:S.375, A:S.375, A:T.376, 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:T.456, A:G.458, A:A.459 Water bridges: A:S.377, A:S.377, A:D.427, A:N.454, B:S.25 TZD.10: 30 residues within 4Å: Chain A: N.22, P.23, G.24, S.25, E.46, A.69, A.72, G.73, N.76, L.109 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 Ligands: CA.7 23 PLIP interactions: 21 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.432, B:L.460, A:A.69 Hydrogen bonds: B:S.375, B:S.375, B:T.376, B:T.376, B:S.377, B:G.400, B:L.402, B:G.426, B:G.428, B:S.429, B:Y.432, B:N.454, B:T.456, B:G.458, B:A.459 Water bridges: B:S.377, B:S.377, B:D.427, B:N.454, A:S.25 TZD.15: 30 residues within 4Å: 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 Chain D: N.22, P.23, G.24, S.25, E.46, A.69, A.72, G.73, N.76, L.109 Ligands: CA.12 23 PLIP interactions: 21 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:Y.432, C:L.460, D:A.69 Hydrogen bonds: C:S.375, C:S.375, C:T.376, 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:T.456, C:G.458, C:A.459 Water bridges: C:S.377, C:S.377, C:D.427, C:N.454, D:S.25 TZD.20: 30 residues within 4Å: Chain C: N.22, P.23, G.24, S.25, E.46, A.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: CA.17 23 PLIP interactions: 21 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:Y.432, D:L.460, C:A.69 Hydrogen bonds: D:S.375, D:S.375, D:T.376, 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:T.456, D:G.458, D:A.459 Water bridges: D:S.377, D:S.377, D:D.427, D:N.454, C:S.25

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bera, A.K. et al., BENZOYLFORMATE DECARBOXYLASE H70A MUTANT at pH 8.5 FROM PSEUDOMONAS PUTIDA. to be published

Release Date

2015-09-23

Peptides

Benzoylformate decarboxylase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Benzoylformate decarboxylase