- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.62 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x D7K: 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-2-{(S)-hydroxy[(R)-hydroxy(methoxy)phosphoryl]phenylmethyl}-5-(2-{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium(Non-covalent)
- 4 x MG: MAGNESIUM ION(Non-covalent)
MG.2: 4 residues within 4Å:- Chain A: D.428, N.455, T.457
- Ligands: D7K.1
3 PLIP interactions:2 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:D.428, A:T.457, H2O.1
MG.9: 4 residues within 4Å:- Chain B: D.428, N.455, T.457
- Ligands: D7K.8
3 PLIP interactions:2 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:D.428, B:T.457, H2O.23
MG.15: 4 residues within 4Å:- Chain C: D.428, N.455, T.457
- Ligands: D7K.14
3 PLIP interactions:2 interactions with chain C, 1 Ligand-Water interactions- Metal complexes: C:D.428, C:T.457, H2O.43
MG.23: 4 residues within 4Å:- Chain D: D.428, N.455, T.457
- Ligands: D7K.22
3 PLIP interactions:2 interactions with chain D, 1 Ligand-Water interactions- Metal complexes: D:D.428, D:T.457, H2O.65
- 11 x CL: CHLORIDE ION(Non-functional Binders)
CL.3: 3 residues within 4Å:- Chain A: N.186, D.187
- Chain D: R.184
Ligand excluded by PLIPCL.4: 3 residues within 4Å:- Chain A: R.184
- Chain D: N.186, D.187
Ligand excluded by PLIPCL.5: 6 residues within 4Å:- Chain A: N.117, L.118, R.120
- Chain B: N.117, L.118, R.120
Ligand excluded by PLIPCL.6: 4 residues within 4Å:- Chain A: Q.421, A.510, L.511, A.513
Ligand excluded by PLIPCL.10: 3 residues within 4Å:- Chain B: N.186, D.187
- Chain C: R.184
Ligand excluded by PLIPCL.11: 3 residues within 4Å:- Chain B: R.184
- Chain C: N.186, D.187
Ligand excluded by PLIPCL.12: 4 residues within 4Å:- Chain B: Q.421, A.510, L.511, A.513
Ligand excluded by PLIPCL.13: 3 residues within 4Å:- Chain B: D.114, A.115, A.116
Ligand excluded by PLIPCL.16: 4 residues within 4Å:- Chain C: Q.421, A.510, L.511, A.513
Ligand excluded by PLIPCL.17: 6 residues within 4Å:- Chain C: N.117, L.118, R.120
- Chain D: N.117, L.118, R.120
Ligand excluded by PLIPCL.24: 4 residues within 4Å:- Chain D: Q.421, A.510, L.511, A.513
Ligand excluded by PLIP- 3 x PO4: PHOSPHATE ION(Non-functional Binders)
PO4.7: 7 residues within 4Å:- Chain A: Q.287, L.289, K.290, P.291
- Chain D: Q.170, H.172, H.173
5 PLIP interactions:3 interactions with chain D, 2 interactions with chain A- Hydrogen bonds: D:Q.170, A:Q.287, A:L.289
- Salt bridges: D:H.172, D:H.173
PO4.18: 7 residues within 4Å:- Chain B: Q.170, H.172, H.173
- Chain C: Q.287, L.289, K.290, P.291
7 PLIP interactions:4 interactions with chain C, 3 interactions with chain B- Hydrogen bonds: C:Q.287, C:L.289, C:L.289, B:Q.170
- Water bridges: C:G.292
- Salt bridges: B:H.172, B:H.173
PO4.19: 7 residues within 4Å:- Chain B: Q.287, L.289, K.290, P.291
- Chain C: Q.170, H.172, H.173
5 PLIP interactions:2 interactions with chain B, 3 interactions with chain C- Hydrogen bonds: B:Q.287, B:K.290, C:Q.170
- Salt bridges: C:H.172, C:H.173
- 3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
PEG.20: 5 residues within 4Å:- Chain C: D.18, E.37, D.38, F.39, R.40
No protein-ligand interaction detected (PLIP)PEG.21: 2 residues within 4Å:- Chain C: A.218, P.392
2 PLIP interactions:2 interactions with chain C- Water bridges: C:N.215, C:N.215
PEG.25: 5 residues within 4Å:- Chain D: D.18, E.37, D.38, F.39, R.40
1 PLIP interactions:1 interactions with chain D- Hydrogen bonds: D:E.37
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Bruning, M. et al., Structural and kinetic studies on native intermediates and an intermediate analogue in benzoylformate decarboxylase reveal a least motion mechanism with an unprecedented short-lived predecarboxylation intermediate. Biochemistry (2009)
- Release Date
- 2009-05-05
- Peptides
- Benzoylformate decarboxylase: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
D
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.62 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x D7K: 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-2-{(S)-hydroxy[(R)-hydroxy(methoxy)phosphoryl]phenylmethyl}-5-(2-{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium(Non-covalent)
- 4 x MG: MAGNESIUM ION(Non-covalent)
- 11 x CL: CHLORIDE ION(Non-functional Binders)
- 3 x PO4: PHOSPHATE ION(Non-functional Binders)
- 3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Bruning, M. et al., Structural and kinetic studies on native intermediates and an intermediate analogue in benzoylformate decarboxylase reveal a least motion mechanism with an unprecedented short-lived predecarboxylation intermediate. Biochemistry (2009)
- Release Date
- 2009-05-05
- Peptides
- Benzoylformate decarboxylase: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
D