- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.30 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.2
MG.7: 4 residues within 4Å:- Chain B: D.442, N.469, G.471
- Ligands: TD6.6
3 PLIP interactions:2 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:D.442, B:G.471, H2O.17
MG.11: 5 residues within 4Å:- Chain C: D.442, N.469, G.471, G.472
- Ligands: TD6.10
3 PLIP interactions:2 interactions with chain C, 1 Ligand-Water interactions- Metal complexes: C:D.442, C:G.471, H2O.36
MG.18: 4 residues within 4Å:- Chain D: D.442, N.469, G.471
- Ligands: TD6.17
3 PLIP interactions:2 interactions with chain D, 1 Ligand-Water interactions- Metal complexes: D:D.442, D:G.471, H2O.48
- 15 x FMT: FORMIC ACID(Non-functional Binders)
FMT.3: 4 residues within 4Å:- Chain A: Q.211, R.212, D.213, R.324
6 PLIP interactions:5 interactions with chain A, 1 interactions with chain C- Hydrogen bonds: A:K.210, A:R.212, A:D.213, A:R.324
- Water bridges: A:R.212, C:R.201
FMT.4: 7 residues within 4Å:- Chain A: G.31, S.32, R.33, T.78, R.107, Q.118
- Ligands: TD6.6
6 PLIP interactions:6 interactions with chain A- Hydrogen bonds: A:S.32, A:R.33, A:R.107, A:Q.118
- Water bridges: A:R.33, A:R.107
FMT.8: 7 residues within 4Å:- Chain B: G.31, S.32, R.33, T.78, R.107, Q.118
- Ligands: TD6.1
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:S.32, B:R.33, B:R.107, B:R.107, B:Q.118
FMT.9: 2 residues within 4Å:- Chain B: Q.186, W.193
No protein-ligand interaction detected (PLIP)FMT.12: 4 residues within 4Å:- Chain C: F.47, I.48, H.49
- Chain D: R.487
3 PLIP interactions:1 interactions with chain C, 2 interactions with chain D- Hydrogen bonds: C:H.49, D:R.487, D:R.487
FMT.13: 2 residues within 4Å:- Chain C: Q.186, W.193
No protein-ligand interaction detected (PLIP)FMT.14: 3 residues within 4Å:- Chain C: R.364, R.375, D.378
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:R.364
FMT.15: 6 residues within 4Å:- Chain C: R.510, P.511, Q.512, E.534, M.535, V.536
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:P.511, C:V.536
FMT.16: 4 residues within 4Å:- Chain C: T.51, R.430, L.454, Q.457
5 PLIP interactions:5 interactions with chain C- Hydrogen bonds: C:T.51, C:R.430, C:R.430
- Water bridges: C:L.454, C:Q.457
FMT.19: 7 residues within 4Å:- Chain D: G.31, S.32, R.33, T.78, R.107, Q.118
- Ligands: TD6.10
7 PLIP interactions:7 interactions with chain D- Hydrogen bonds: D:S.32, D:R.33, D:T.78, D:T.78, D:R.107, D:R.107, D:Q.118
FMT.20: 2 residues within 4Å:- Chain D: D.213, F.216
1 PLIP interactions:1 interactions with chain D- Hydrogen bonds: D:D.213
FMT.21: 2 residues within 4Å:- Chain D: Q.186, W.193
1 PLIP interactions:1 interactions with chain D- Hydrogen bonds: D:Q.186
FMT.22: 5 residues within 4Å:- Chain D: E.505, L.506, K.507, T.529, T.530
3 PLIP interactions:3 interactions with chain D- Hydrogen bonds: D:K.507, D:T.529
- Water bridges: D:E.505
FMT.23: 4 residues within 4Å:- Chain D: T.51, R.430, L.454, Q.457
6 PLIP interactions:2 interactions with chain C, 4 interactions with chain D- Water bridges: C:Q.493, C:Q.493
- Hydrogen bonds: D:T.51, D:R.430, D:R.430, D:Q.457
FMT.24: 5 residues within 4Å:- Chain D: E.16, R.20, W.193, Q.194, D.195
3 PLIP interactions:3 interactions with chain D- Water bridges: D:E.16, D:E.16, D:T.19
- 1 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
CD
D
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.30 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)
- 15 x FMT: FORMIC ACID(Non-functional Binders)
- 1 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
CD
D