- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.50 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x N2P: PENTANE-1,5-DIAMINE(Non-covalent)
- 2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Non-covalent)
PLP.2: 13 residues within 4Å:- Chain A: A.49, K.51, D.70, H.179, S.182, G.218, G.219, E.255, G.257, R.258, Y.352
- Chain B: C.323
- Ligands: N2P.1
13 PLIP interactions:13 interactions with chain A- Hydrophobic interactions: A:A.49, A:K.51
- Hydrogen bonds: A:K.51, A:D.70, A:G.219, A:G.257, A:R.258, A:Y.352, A:Y.352
- Water bridges: A:F.220
- Salt bridges: A:H.179, A:R.258
- pi-Stacking: A:H.179
PLP.10: 13 residues within 4Å:- Chain A: C.323
- Chain B: A.49, K.51, D.70, H.179, S.182, G.218, G.219, E.255, G.257, R.258, Y.352
- Ligands: N2P.9
12 PLIP interactions:12 interactions with chain B- Hydrophobic interactions: B:A.49, B:K.51
- Hydrogen bonds: B:K.51, B:G.219, B:G.257, B:R.258, B:Y.352, B:Y.352
- Water bridges: B:F.220
- Salt bridges: B:H.179, B:R.258
- pi-Stacking: B:H.179
- 4 x GOL: GLYCEROL(Non-functional Binders)
GOL.3: 6 residues within 4Å:- Chain A: V.271, I.272, I.340, G.341
- Chain B: A.99, K.123
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:A.99
GOL.4: 7 residues within 4Å:- Chain A: K.2, F.4, S.26, D.28, E.32, R.380
- Ligands: PGE.5
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:S.26, A:E.32, A:R.380
GOL.11: 6 residues within 4Å:- Chain A: A.99, K.123
- Chain B: V.271, I.272, I.340, G.341
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:A.99
GOL.12: 7 residues within 4Å:- Chain B: K.2, F.4, S.26, D.28, E.32, R.380
- Ligands: PGE.13
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:S.26, B:E.32, B:R.380
- 2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)
PGE.5: 10 residues within 4Å:- Chain A: M.1, K.29, E.32, N.33, F.36, P.223, L.232, Y.259, T.263
- Ligands: GOL.4
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:M.1, A:K.29, A:E.32
PGE.13: 10 residues within 4Å:- Chain B: M.1, K.29, E.32, N.33, F.36, P.223, L.232, Y.259, T.263
- Ligands: GOL.12
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:K.29, B:E.32, B:E.32
- 4 x NA: SODIUM ION(Non-functional Binders)
NA.6: 3 residues within 4Å:- Chain A: H.306, T.347, E.348
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:E.348
NA.7: 0 residues within 4Å:- (No contacts)
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:L.83
NA.14: 3 residues within 4Å:- Chain B: H.306, T.347, E.348
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:T.347, B:E.348
NA.15: 0 residues within 4Å:- (No contacts)
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:L.83
- 2 x MG: MAGNESIUM ION(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Sagong, H.-Y. et al., Crystal Structure and Pyridoxal 5-Phosphate Binding Property of Lysine Decarboxylase from Selenomonas ruminantium. PLoS ONE (2016)
- Release Date
- 2016-11-23
- Peptides
- Lysine/ornithine decarboxylase: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
A
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.50 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x N2P: PENTANE-1,5-DIAMINE(Non-covalent)
- 2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Non-covalent)
- 4 x GOL: GLYCEROL(Non-functional Binders)
- 2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)
- 4 x NA: SODIUM ION(Non-functional Binders)
- 2 x MG: MAGNESIUM ION(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Sagong, H.-Y. et al., Crystal Structure and Pyridoxal 5-Phosphate Binding Property of Lysine Decarboxylase from Selenomonas ruminantium. PLoS ONE (2016)
- Release Date
- 2016-11-23
- Peptides
- Lysine/ornithine decarboxylase: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
A