- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.35 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x TD6: (4S)-4-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3lambda~5~-thiazol-2-yl}-4-hydroxybutanoic acid(Non-covalent)
- 4 x MG: MAGNESIUM ION(Non-covalent)
MG.2: 4 residues within 4Å:- Chain A: D.442, N.469, G.471
- Ligands: TD6.1
3 PLIP interactions:2 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:D.442, A:G.471, H2O.5
MG.4: 4 residues within 4Å:- Chain B: D.442, N.469, G.471
- Ligands: TD6.3
3 PLIP interactions:2 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:D.442, B:G.471, H2O.18
MG.8: 4 residues within 4Å:- Chain C: D.442, N.469, G.471
- Ligands: TD6.7
3 PLIP interactions:2 interactions with chain C, 1 Ligand-Water interactions- Metal complexes: C:D.442, C:G.471, H2O.36
MG.12: 4 residues within 4Å:- Chain D: D.442, N.469, G.471
- Ligands: TD6.11
3 PLIP interactions:2 interactions with chain D, 1 Ligand-Water interactions- Metal complexes: D:D.442, D:G.471, H2O.57
- 4 x FMT: FORMIC ACID(Non-functional Binders)
FMT.5: 4 residues within 4Å:- Chain B: K.70, R.228, M.229, S.230
3 PLIP interactions:3 interactions with chain B- Water bridges: B:R.228, B:R.228, B:S.230
FMT.6: 3 residues within 4Å:- Chain B: Q.186, Q.187, W.193
1 PLIP interactions:1 interactions with chain B- Water bridges: B:Q.187
FMT.10: 4 residues within 4Å:- Chain C: S.208, E.209, Q.211
- Chain D: A.203
4 PLIP interactions:2 interactions with chain D, 2 interactions with chain C- Water bridges: D:A.203, D:A.203
- Hydrogen bonds: C:E.209, C:Q.211
FMT.14: 4 residues within 4Å:- Chain D: R.364, H.374, R.375, D.378
1 PLIP interactions:1 interactions with chain D- Hydrogen bonds: D:R.364
- 2 x GOL: GLYCEROL(Non-functional Binders)
GOL.9: 5 residues within 4Å:- Chain C: E.16, N.44, S.45, A.46, W.193
8 PLIP interactions:8 interactions with chain C- Hydrogen bonds: C:T.19, C:R.20, C:N.44, C:N.44, C:S.45, C:S.45, C:A.46, C:W.193
GOL.13: 6 residues within 4Å:- Chain D: H.49, H.50, T.51, R.430, L.454, Q.457
8 PLIP interactions:7 interactions with chain D, 1 interactions with chain A- Hydrogen bonds: D:T.51, D:R.430, D:R.430
- Water bridges: D:H.50, D:A.453, D:L.454, D:Q.457, A:Q.493
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Qin, M.M. et al., Two active site arginines are critical determinants of substrate binding and catalysis in MenD: a thiamine-dependent enzyme in menaquinone biosynthesis. Biochem. J. (2018)
- Release Date
- 2018-11-28
- Peptides
- 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
GD
H
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.35 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x TD6: (4S)-4-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3lambda~5~-thiazol-2-yl}-4-hydroxybutanoic acid(Non-covalent)
- 4 x MG: MAGNESIUM ION(Non-covalent)
- 4 x FMT: FORMIC ACID(Non-functional Binders)
- 2 x GOL: GLYCEROL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Qin, M.M. et al., Two active site arginines are critical determinants of substrate binding and catalysis in MenD: a thiamine-dependent enzyme in menaquinone biosynthesis. Biochem. J. (2018)
- Release Date
- 2018-11-28
- Peptides
- 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
GD
H