- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.72 Å
- Oligo State
- homo-dimer
- Ligands
- 8 x GOL: GLYCEROL(Non-functional Binders)
- 2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)
PLP.4: 15 residues within 4Å:- Chain A: A.73, K.75, H.117, R.164, H.214, H.216, G.256, G.257, E.299, P.300, G.301, R.302, Y.404
- Chain B: C.374
- Ligands: LYS.5
20 PLIP interactions:16 interactions with chain A, 1 interactions with chain B, 3 Ligand-Ligand interactions- Hydrophobic interactions: A:A.73, A:K.75, K.5
- Hydrogen bonds: A:K.75, A:G.257, A:Y.258, A:G.301, A:R.302, A:Y.404, A:Y.404, K.5
- Water bridges: A:R.302, A:R.302, A:A.303, B:C.374, K.5
- Salt bridges: A:K.75, A:H.216, A:R.302
- pi-Stacking: A:H.216
PLP.11: 14 residues within 4Å:- Chain A: C.374
- Chain B: A.73, K.75, H.117, R.164, H.216, G.256, G.257, E.299, P.300, G.301, R.302, Y.404
- Ligands: LYS.12
16 PLIP interactions:15 interactions with chain B, 1 interactions with chain A- Hydrophobic interactions: B:A.73, B:K.75
- Hydrogen bonds: B:G.257, B:E.299, B:G.301, B:R.302, B:Y.404
- Water bridges: B:R.164, B:Y.258, B:Y.258, B:R.302, A:C.374
- Salt bridges: B:K.75, B:H.216, B:R.302
- pi-Stacking: B:H.216
- 2 x LYS: LYSINE(Non-covalent)
LYS.5: 11 residues within 4Å:- Chain A: K.75, H.216, R.302, R.343, Y.347, Y.404, M.408
- Chain B: C.374, E.375, Y.412
- Ligands: PLP.4
6 PLIP interactions:6 interactions with chain A,- Hydrophobic interactions: A:Y.404
- Hydrogen bonds: A:K.75, A:R.302, A:R.343, A:Y.347
- Salt bridges: A:R.343
LYS.12: 10 residues within 4Å:- Chain A: C.374, E.375, Y.412
- Chain B: K.75, R.302, R.343, Y.347, Y.404, M.408
- Ligands: PLP.11
9 PLIP interactions:5 interactions with chain B, 2 interactions with chain A, 2 Ligand-Ligand interactions- Hydrophobic interactions: B:Y.404
- Hydrogen bonds: B:K.75, B:R.343, A:C.374, A:Y.412, K.12, K.12
- Salt bridges: B:R.302, B:R.343
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Son, H.F. et al., Structural basis for substrate specificity of meso-diaminopimelic acid decarboxylase from Corynebacterium glutamicum. Biochem. Biophys. Res. Commun. (2018)
- Release Date
- 2018-01-10
- Peptides
- Diaminopimelate decarboxylase: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.72 Å
- Oligo State
- homo-dimer
- Ligands
- 8 x GOL: GLYCEROL(Non-functional Binders)
- 2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)
- 2 x LYS: LYSINE(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Son, H.F. et al., Structural basis for substrate specificity of meso-diaminopimelic acid decarboxylase from Corynebacterium glutamicum. Biochem. Biophys. Res. Commun. (2018)
- Release Date
- 2018-01-10
- Peptides
- Diaminopimelate decarboxylase: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B