- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.30 Å
- Oligo State
- homo-hexamer
- Ligands
- 6 x MG: MAGNESIUM ION(Non-covalent)
- 12 x C: CYTIDINE-5'-MONOPHOSPHATE(Non-covalent)
C.2: 16 residues within 4Å:- Chain A: H.243, D.265, I.266, G.267, E.268
- Chain B: A.309, P.312, K.313, L.314, K.315, K.318, A.340, T.341, T.342, E.344
- Ligands: MG.1
84 PLIP interactions:24 interactions with chain B, 4 interactions with chain E, 4 interactions with chain F, 24 interactions with chain A, 24 interactions with chain C, 4 interactions with chain D- Hydrophobic interactions: B:A.340, B:T.342, A:A.340, A:T.342, C:A.340, C:T.342
- Hydrogen bonds: B:A.11, B:T.53, B:G.73, B:S.79, B:V.97, B:D.265, B:G.267, B:E.268, B:E.268, B:A.309, B:K.313, B:L.314, B:K.315, B:K.318, B:T.342, B:E.344, A:A.11, A:T.53, A:G.73, A:S.79, A:V.97, A:D.265, A:G.267, A:E.268, A:E.268, A:A.309, A:K.313, A:L.314, A:K.315, A:K.318, A:T.342, A:E.344, C:A.11, C:T.53, C:G.73, C:S.79, C:V.97, C:D.265, C:G.267, C:E.268, C:E.268, C:A.309, C:K.313, C:L.314, C:K.315, C:K.318, C:T.342, C:E.344
- Water bridges: B:S.14, B:Q.24, B:T.342, B:T.342, E:R.139, E:R.139, E:R.139, F:R.139, F:R.139, F:R.139, A:S.14, A:Q.24, A:T.342, A:T.342, C:S.14, C:Q.24, C:T.342, C:T.342, D:R.139, D:R.139, D:R.139
- Salt bridges: B:K.191, B:H.243, E:R.139, F:R.139, A:K.191, A:H.243, C:K.191, C:H.243, D:R.139
C.3: 13 residues within 4Å:- Chain A: L.9, A.10, A.11, T.53, G.73, D.74, T.75, R.76, S.79, D.96, V.97, K.191
- Chain D: R.139
Protein-ligand interaction information (PLIP) not availableC.7: 16 residues within 4Å:- Chain B: H.243, D.265, I.266, G.267, E.268
- Chain C: A.309, P.312, K.313, L.314, K.315, K.318, A.340, T.341, T.342, E.344
- Ligands: MG.6
Protein-ligand interaction information (PLIP) not availableC.8: 13 residues within 4Å:- Chain B: L.9, A.10, A.11, T.53, G.73, D.74, T.75, R.76, S.79, D.96, V.97, K.191
- Chain F: R.139
Protein-ligand interaction information (PLIP) not availableC.12: 16 residues within 4Å:- Chain A: A.309, P.312, K.313, L.314, K.315, K.318, A.340, T.341, T.342, E.344
- Chain C: H.243, D.265, I.266, G.267, E.268
- Ligands: MG.11
Protein-ligand interaction information (PLIP) not availableC.13: 13 residues within 4Å:- Chain C: L.9, A.10, A.11, T.53, G.73, D.74, T.75, R.76, S.79, D.96, V.97, K.191
- Chain E: R.139
Protein-ligand interaction information (PLIP) not availableC.17: 16 residues within 4Å:- Chain D: H.243, D.265, I.266, G.267, E.268
- Chain E: A.309, P.312, K.313, L.314, K.315, K.318, A.340, T.341, T.342, E.344
- Ligands: MG.16
84 PLIP interactions:24 interactions with chain E, 24 interactions with chain D, 24 interactions with chain F, 4 interactions with chain B, 4 interactions with chain A, 4 interactions with chain C- Hydrophobic interactions: E:A.340, E:T.342, D:A.340, D:T.342, F:A.340, F:T.342
- Hydrogen bonds: E:A.11, E:G.73, E:S.79, E:V.97, E:D.265, E:G.267, E:E.268, E:A.309, E:K.313, E:L.314, E:K.315, E:K.318, E:T.341, E:T.342, E:E.344, E:E.344, D:A.11, D:G.73, D:S.79, D:V.97, D:D.265, D:G.267, D:E.268, D:A.309, D:K.313, D:L.314, D:K.315, D:K.318, D:T.341, D:T.342, D:E.344, D:E.344, F:A.11, F:G.73, F:S.79, F:V.97, F:D.265, F:G.267, F:E.268, F:A.309, F:K.313, F:L.314, F:K.315, F:K.318, F:T.341, F:T.342, F:E.344, F:E.344
- Water bridges: E:S.14, E:Q.24, E:T.342, E:T.342, D:S.14, D:Q.24, D:T.342, D:T.342, F:S.14, F:Q.24, F:T.342, F:T.342, B:R.139, B:R.139, B:R.139, A:R.139, A:R.139, A:R.139, C:R.139, C:R.139, C:R.139
- Salt bridges: E:K.191, E:H.243, D:K.191, D:H.243, F:K.191, F:H.243, B:R.139, A:R.139, C:R.139
C.18: 13 residues within 4Å:- Chain A: R.139
- Chain D: L.9, A.10, A.11, T.53, G.73, D.74, T.75, R.76, S.79, D.96, V.97, K.191
Protein-ligand interaction information (PLIP) not availableC.22: 16 residues within 4Å:- Chain E: H.243, D.265, I.266, G.267, E.268
- Chain F: A.309, P.312, K.313, L.314, K.315, K.318, A.340, T.341, T.342, E.344
- Ligands: MG.21
Protein-ligand interaction information (PLIP) not availableC.23: 13 residues within 4Å:- Chain C: R.139
- Chain E: L.9, A.10, A.11, T.53, G.73, D.74, T.75, R.76, S.79, D.96, V.97, K.191
Protein-ligand interaction information (PLIP) not availableC.27: 16 residues within 4Å:- Chain D: A.309, P.312, K.313, L.314, K.315, K.318, A.340, T.341, T.342, E.344
- Chain F: H.243, D.265, I.266, G.267, E.268
- Ligands: MG.26
Protein-ligand interaction information (PLIP) not availableC.28: 13 residues within 4Å:- Chain B: R.139
- Chain F: L.9, A.10, A.11, T.53, G.73, D.74, T.75, R.76, S.79, D.96, V.97, K.191
Protein-ligand interaction information (PLIP) not available- 6 x GPP: GERANYL DIPHOSPHATE(Non-covalent)
GPP.4: 17 residues within 4Å:- Chain A: F.216, M.308, G.347, F.348, R.351
- Chain B: F.216, M.308, G.347, F.348, R.351
- Chain C: F.216, M.308, G.347, F.348, R.351
- Ligands: GPP.9, GPP.14
17 PLIP interactions:8 interactions with chain B, 4 interactions with chain C, 5 interactions with chain A- Hydrophobic interactions: B:F.216, B:F.216, B:F.348, C:F.216, A:F.348
- Hydrogen bonds: B:G.347, B:F.348, C:F.348, A:F.348
- Water bridges: B:I.349, B:R.351, C:I.349, A:I.349, A:E.353
- Salt bridges: B:R.351, C:R.351, A:R.351
GPP.9: 17 residues within 4Å:- Chain A: F.216, M.308, G.347, F.348, R.351
- Chain B: F.216, M.308, G.347, F.348, R.351
- Chain C: F.216, M.308, G.347, F.348, R.351
- Ligands: GPP.4, GPP.14
17 PLIP interactions:5 interactions with chain B, 8 interactions with chain C, 4 interactions with chain A- Hydrophobic interactions: B:F.348, C:F.216, C:F.216, C:F.348, A:F.216
- Hydrogen bonds: B:F.348, C:G.347, C:F.348, A:F.348
- Water bridges: B:I.349, B:E.353, C:I.349, C:R.351, A:I.349
- Salt bridges: B:R.351, C:R.351, A:R.351
GPP.14: 17 residues within 4Å:- Chain A: F.216, M.308, G.347, F.348, R.351
- Chain B: F.216, M.308, G.347, F.348, R.351
- Chain C: F.216, M.308, G.347, F.348, R.351
- Ligands: GPP.4, GPP.9
17 PLIP interactions:4 interactions with chain B, 8 interactions with chain A, 5 interactions with chain C- Hydrophobic interactions: B:F.216, A:F.216, A:F.216, A:F.348, C:F.348
- Hydrogen bonds: B:F.348, A:G.347, A:F.348, C:F.348
- Water bridges: B:I.349, A:I.349, A:R.351, C:I.349, C:E.353
- Salt bridges: B:R.351, A:R.351, C:R.351
GPP.19: 17 residues within 4Å:- Chain D: F.216, M.308, G.347, F.348, R.351
- Chain E: F.216, M.308, G.347, F.348, R.351
- Chain F: F.216, M.308, G.347, F.348, R.351
- Ligands: GPP.24, GPP.29
17 PLIP interactions:8 interactions with chain E, 5 interactions with chain D, 4 interactions with chain F- Hydrophobic interactions: E:F.216, E:F.216, E:F.348, D:F.348, F:F.216
- Hydrogen bonds: E:G.347, E:F.348, D:F.348, F:F.348
- Water bridges: E:I.349, E:R.351, D:I.349, D:E.353, F:I.349
- Salt bridges: E:R.351, D:R.351, F:R.351
GPP.24: 17 residues within 4Å:- Chain D: F.216, M.308, G.347, F.348, R.351
- Chain E: F.216, M.308, G.347, F.348, R.351
- Chain F: F.216, M.308, G.347, F.348, R.351
- Ligands: GPP.19, GPP.29
17 PLIP interactions:5 interactions with chain E, 4 interactions with chain D, 8 interactions with chain F- Hydrophobic interactions: E:F.348, D:F.216, F:F.216, F:F.216, F:F.348
- Hydrogen bonds: E:F.348, D:F.348, F:G.347, F:F.348
- Water bridges: E:I.349, E:E.353, D:I.349, F:I.349, F:R.351
- Salt bridges: E:R.351, D:R.351, F:R.351
GPP.29: 17 residues within 4Å:- Chain D: F.216, M.308, G.347, F.348, R.351
- Chain E: F.216, M.308, G.347, F.348, R.351
- Chain F: F.216, M.308, G.347, F.348, R.351
- Ligands: GPP.19, GPP.24
17 PLIP interactions:4 interactions with chain E, 5 interactions with chain F, 8 interactions with chain D- Hydrophobic interactions: E:F.216, F:F.348, D:F.216, D:F.216, D:F.348
- Hydrogen bonds: E:F.348, F:F.348, D:G.347, D:F.348
- Water bridges: E:I.349, F:I.349, F:E.353, D:I.349, D:R.351
- Salt bridges: E:R.351, F:R.351, D:R.351
- 6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.5: 8 residues within 4Å:- Chain A: D.128, T.129
- Chain D: D.96, R.99, I.145, T.167, D.168, K.191
7 PLIP interactions:4 interactions with chain D, 3 interactions with chain A- Hydrogen bonds: D:D.96, D:R.99, D:I.145, D:K.191, A:T.129, A:T.129
- Water bridges: A:R.139
EDO.10: 8 residues within 4Å:- Chain B: D.128, T.129
- Chain F: D.96, R.99, I.145, T.167, D.168, K.191
7 PLIP interactions:4 interactions with chain F, 3 interactions with chain B- Hydrogen bonds: F:D.96, F:R.99, F:I.145, F:K.191, B:T.129, B:T.129
- Water bridges: B:R.139
EDO.15: 8 residues within 4Å:- Chain C: D.128, T.129
- Chain E: D.96, R.99, I.145, T.167, D.168, K.191
7 PLIP interactions:3 interactions with chain C, 4 interactions with chain E- Hydrogen bonds: C:T.129, C:T.129, E:D.96, E:R.99, E:I.145, E:K.191
- Water bridges: C:R.139
EDO.20: 8 residues within 4Å:- Chain A: D.96, R.99, I.145, T.167, D.168, K.191
- Chain D: D.128, T.129
6 PLIP interactions:2 interactions with chain D, 4 interactions with chain A- Hydrogen bonds: D:T.129, A:D.96, A:R.99, A:I.145, A:K.191
- Water bridges: D:R.139
EDO.25: 8 residues within 4Å:- Chain C: D.96, R.99, I.145, T.167, D.168, K.191
- Chain E: D.128, T.129
6 PLIP interactions:4 interactions with chain C, 2 interactions with chain E- Hydrogen bonds: C:D.96, C:R.99, C:I.145, C:K.191, E:T.129
- Water bridges: E:R.139
EDO.30: 8 residues within 4Å:- Chain B: D.96, R.99, I.145, T.167, D.168, K.191
- Chain F: D.128, T.129
6 PLIP interactions:2 interactions with chain F, 4 interactions with chain B- Hydrogen bonds: F:T.129, B:D.96, B:R.99, B:I.145, B:K.191
- Water bridges: F:R.139
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Gabrielsen, M. et al., Hexameric Assembly of the Bifunctional Methylerythritol 2,4-Cyclodiphosphate Synthase and Protein-Protein Associations in the Deoxy-Xylulose-Dependent Pathway of Isoprenoid Precursor Biosynthesis. J.Biol.Chem. (2004)
- Release Date
- 2004-10-04
- Peptides
- ISPD/ISPF BIFUNCTIONAL ENZYME: ABCDEF
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
AC
AD
AE
AF
A
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.30 Å
- Oligo State
- homo-hexamer
- Ligands
- 6 x MG: MAGNESIUM ION(Non-covalent)
- 12 x C: CYTIDINE-5'-MONOPHOSPHATE(Non-covalent)
- 6 x GPP: GERANYL DIPHOSPHATE(Non-covalent)
- 6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Gabrielsen, M. et al., Hexameric Assembly of the Bifunctional Methylerythritol 2,4-Cyclodiphosphate Synthase and Protein-Protein Associations in the Deoxy-Xylulose-Dependent Pathway of Isoprenoid Precursor Biosynthesis. J.Biol.Chem. (2004)
- Release Date
- 2004-10-04
- Peptides
- ISPD/ISPF BIFUNCTIONAL ENZYME: ABCDEF
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
AC
AD
AE
AF
A