- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.60 Å
- Oligo State
- homo-tetramer
- Ligands
- 6 x NA: SODIUM ION(Non-functional Binders)
- 4 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)
TPP.3: 22 residues within 4Å:- Chain A: S.391, L.392, S.416, G.417, I.418, D.419, G.441, D.442, L.443, S.444, Y.447, N.469, G.471, G.472, Q.473, I.474, F.475
- Chain B: P.30, E.55, T.81, A.82
- Ligands: MG.4
24 PLIP interactions:20 interactions with chain A, 4 interactions with chain B- Hydrophobic interactions: A:I.418, A:I.418, A:D.419, A:Y.447, A:F.475, B:P.30, B:A.82
- Hydrogen bonds: A:S.391, A:S.391, A:L.392, A:S.416, A:I.418, A:D.442, A:L.443, A:S.444, A:N.469, A:N.469, A:Q.473, A:I.474
- Water bridges: A:V.393, A:G.441, B:A.82, B:Q.118
- pi-Stacking: A:F.475
TPP.6: 22 residues within 4Å:- Chain A: P.30, E.55, T.78, T.81, A.82, Q.118
- Chain B: S.391, L.392, S.416, G.417, I.418, D.419, G.441, D.442, L.443, S.444, N.469, G.471, G.472, Q.473, I.474
- Ligands: MG.7
14 PLIP interactions:12 interactions with chain B, 2 interactions with chain A- Hydrophobic interactions: B:D.419, B:I.474, A:P.30
- Hydrogen bonds: B:S.391, B:L.392, B:S.416, B:I.418, B:L.443, B:S.444, B:N.469, B:G.472, B:Q.473, B:I.474, A:T.81
TPP.11: 23 residues within 4Å:- Chain C: S.391, L.392, S.416, G.417, I.418, D.419, G.441, D.442, L.443, S.444, Y.447, N.469, G.471, G.472, Q.473, I.474, F.475
- Chain D: P.30, E.55, T.78, T.81, A.82
- Ligands: MG.12
19 PLIP interactions:17 interactions with chain C, 2 interactions with chain D- Hydrophobic interactions: C:I.418, C:I.418, C:D.419, C:Y.447, D:P.30, D:A.82
- Hydrogen bonds: C:S.391, C:S.391, C:L.392, C:S.416, C:I.418, C:G.441, C:D.442, C:L.443, C:S.444, C:N.469, C:N.469, C:Q.473, C:I.474
TPP.14: 23 residues within 4Å:- Chain C: P.30, E.55, T.78, T.81, A.82
- Chain D: S.391, L.392, S.416, G.417, I.418, D.419, G.441, D.442, L.443, S.444, Y.447, N.469, G.471, G.472, Q.473, I.474, F.475
- Ligands: MG.15
19 PLIP interactions:2 interactions with chain C, 17 interactions with chain D- Hydrophobic interactions: C:P.30, C:T.78, D:I.418, D:D.419, D:Y.447, D:I.474, D:F.475
- Hydrogen bonds: D:S.391, D:L.392, D:S.416, D:I.418, D:D.442, D:L.443, D:S.444, D:N.469, D:N.469, D:G.472, D:Q.473, D:I.474
- 4 x MG: MAGNESIUM ION(Non-covalent)
MG.4: 5 residues within 4Å:- Chain A: D.442, N.469, G.471, G.472
- Ligands: TPP.3
3 PLIP interactions:2 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:D.442, A:G.471, H2O.1
MG.7: 4 residues within 4Å:- Chain B: D.442, N.469, G.471
- Ligands: TPP.6
2 PLIP interactions:2 interactions with chain B- Metal complexes: B:D.442, B:G.471
MG.12: 4 residues within 4Å:- Chain C: D.442, N.469, G.471
- Ligands: TPP.11
2 PLIP interactions:2 interactions with chain C- Metal complexes: C:D.442, C:G.471
MG.15: 5 residues within 4Å:- Chain D: D.442, N.469, G.471, Q.473
- Ligands: TPP.14
2 PLIP interactions:2 interactions with chain D- Metal complexes: D:D.442, D:G.471
- 1 x GOL: GLYCEROL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Priyadarshi, A. et al., Structural and functional analysis of Vitamin K2 synthesis protein MenD. Biochem.Biophys.Res.Commun. (2009)
- Release Date
- 2009-11-03
- Peptides
- 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
ID
J
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.60 Å
- Oligo State
- homo-tetramer
- Ligands
- 6 x NA: SODIUM ION(Non-functional Binders)
- 4 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)
- 4 x MG: MAGNESIUM ION(Non-covalent)
- 1 x GOL: GLYCEROL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Priyadarshi, A. et al., Structural and functional analysis of Vitamin K2 synthesis protein MenD. Biochem.Biophys.Res.Commun. (2009)
- Release Date
- 2009-11-03
- Peptides
- 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
ID
J