- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.00 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x THG: (6S)-5,6,7,8-TETRAHYDROFOLATE(Non-covalent)
- 2 x DHB: 3,4-DIHYDROXYBENZOIC ACID(Non-covalent)
DHB.2: 12 residues within 4Å:- Chain A: Y.32, Y.34, H.63, M.64, R.125, Y.250, P.251, N.253, W.259, P.261, F.396
- Ligands: THG.1
10 PLIP interactions:10 interactions with chain A- Hydrophobic interactions: A:Y.34, A:P.261, A:P.261
- Hydrogen bonds: A:Y.34, A:Y.34, A:Q.60, A:Y.250, A:N.253
- Salt bridges: A:R.125
- pi-Stacking: A:W.259
DHB.7: 11 residues within 4Å:- Chain B: Y.32, Y.34, H.63, M.64, R.125, Y.250, P.251, N.253, W.259, P.261
- Ligands: THG.6
9 PLIP interactions:9 interactions with chain B- Hydrophobic interactions: B:Y.34, B:P.261, B:P.261
- Hydrogen bonds: B:Y.34, B:H.63, B:Y.250, B:N.253
- Salt bridges: B:R.125
- pi-Stacking: B:W.259
- 4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.3: 7 residues within 4Å:- Chain A: G.292, G.293, N.374, Y.375, A.376, N.379, D.381
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:Y.375, A:A.376, A:D.381
EDO.4: 8 residues within 4Å:- Chain A: L.264, Y.268, Y.285, E.286, G.289, A.290, N.377, T.378
6 PLIP interactions:6 interactions with chain A- Hydrogen bonds: A:Y.285, A:G.289, A:A.290, A:A.290, A:N.377, A:T.378
EDO.8: 7 residues within 4Å:- Chain B: G.292, G.293, N.374, Y.375, A.376, N.379, D.381
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:Y.375, B:A.376, B:N.379, B:A.380, B:D.381
EDO.9: 8 residues within 4Å:- Chain B: L.264, Y.268, Y.285, E.286, G.289, A.290, N.377, T.378
6 PLIP interactions:6 interactions with chain B- Hydrogen bonds: B:Y.285, B:G.289, B:A.290, B:N.377, B:T.378, B:T.378
- 2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)
TRS.5: 8 residues within 4Å:- Chain A: G.431, G.432, T.433, R.434, K.435, V.438, E.439, P.440
4 PLIP interactions:1 interactions with chain B, 3 interactions with chain A- Water bridges: B:T.46, A:V.438
- Hydrogen bonds: A:G.431, A:V.438
TRS.10: 8 residues within 4Å:- Chain B: G.431, G.432, T.433, R.434, K.435, V.438, E.439, P.440
3 PLIP interactions:2 interactions with chain B, 1 interactions with chain A- Hydrogen bonds: B:G.431, B:V.438
- Water bridges: A:T.46
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Harada, A. et al., The crystal structure of a new O-demethylase from Sphingobium sp. strain SYK-6. FEBS J. (2017)
- Release Date
- 2017-05-17
- Peptides
- Vanillate/3-O-methylgallate O-demethylase: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.00 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x THG: (6S)-5,6,7,8-TETRAHYDROFOLATE(Non-covalent)
- 2 x DHB: 3,4-DIHYDROXYBENZOIC ACID(Non-covalent)
- 4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Harada, A. et al., The crystal structure of a new O-demethylase from Sphingobium sp. strain SYK-6. FEBS J. (2017)
- Release Date
- 2017-05-17
- Peptides
- Vanillate/3-O-methylgallate O-demethylase: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B