- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.50 Å
- Oligo State
- homo-trimer
- Ligands
- 3 x ZN: ZINC ION(Non-covalent)
- 4 x MG: MAGNESIUM ION(Non-covalent)
MG.2: 3 residues within 4Å:- Chain A: D.11
- Chain C: T.135
- Ligands: ZN.1
4 PLIP interactions:1 interactions with chain C, 1 interactions with chain A, 2 Ligand-Water interactions- Metal complexes: C:T.135, A:D.11, H2O.1, H2O.3
MG.3: 4 residues within 4Å:- Chain A: T.135, E.138
- Chain B: D.11
- Ligands: ZN.9
No protein-ligand interaction detected (PLIP)MG.10: 3 residues within 4Å:- Chain A: E.152
- Chain B: E.152
- Chain C: E.152
5 PLIP interactions:1 interactions with chain B, 2 interactions with chain A, 2 interactions with chain C- Metal complexes: B:E.152, A:E.152, A:E.152, C:E.152, C:E.152
MG.17: 4 residues within 4Å:- Chain B: T.135
- Chain C: D.11
- Ligands: CTN.11, ZN.16
4 PLIP interactions:1 interactions with chain C, 1 interactions with chain B, 2 Ligand-Water interactions- Metal complexes: C:D.11, B:T.135, H2O.2, H2O.2
- 3 x CTN: 4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE(Non-covalent)
CTN.4: 11 residues within 4Å:- Chain A: A.103, P.106, K.107, M.108, L.109, A.134, T.135, T.136
- Chain B: D.59, G.61
- Ligands: EDO.8
6 PLIP interactions:5 interactions with chain A, 1 interactions with chain B- Hydrophobic interactions: A:T.136
- Hydrogen bonds: A:A.103, A:M.108, A:L.109, A:T.135, B:G.61
CTN.11: 13 residues within 4Å:- Chain B: A.103, P.106, K.107, M.108, L.109, A.134, T.135, T.136
- Chain C: D.59, G.61, K.62
- Ligands: EDO.13, MG.17
8 PLIP interactions:2 interactions with chain C, 6 interactions with chain B- Hydrogen bonds: C:G.61, C:K.62, B:P.106, B:M.108, B:L.109, B:A.134
- Hydrophobic interactions: B:A.134, B:T.136
CTN.18: 13 residues within 4Å:- Chain A: D.59, G.61, K.62
- Chain C: A.103, A.105, P.106, K.107, M.108, L.109, A.134, T.135, T.136
- Ligands: EDO.20
5 PLIP interactions:5 interactions with chain C- Hydrogen bonds: C:A.103, C:M.108, C:L.109
- Water bridges: C:T.135, C:T.135
- 1 x POP: PYROPHOSPHATE 2-(Non-covalent)
POP.5: 12 residues within 4Å:- Chain A: G.141, F.142, R.145
- Chain B: G.141, F.142, R.145
- Chain C: G.141, F.142, R.145
- Ligands: EDO.6, EDO.12, EDO.19
6 PLIP interactions:2 interactions with chain A, 2 interactions with chain B, 2 interactions with chain C- Hydrogen bonds: A:F.142, B:F.142, C:F.142
- Salt bridges: A:R.145, B:R.145, C:R.145
- 9 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.6: 4 residues within 4Å:- Chain A: F.142
- Chain B: F.142
- Ligands: POP.5, EDO.12
No protein-ligand interaction detected (PLIP)EDO.7: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)EDO.8: 3 residues within 4Å:- Chain A: Q.104, K.107
- Ligands: CTN.4
No protein-ligand interaction detected (PLIP)EDO.12: 3 residues within 4Å:- Chain B: F.142
- Ligands: POP.5, EDO.6
No protein-ligand interaction detected (PLIP)EDO.13: 3 residues within 4Å:- Chain B: Q.104, K.107
- Ligands: CTN.11
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:Q.104
EDO.14: 2 residues within 4Å:- Chain B: G.124, H.126
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:G.124, B:H.126
EDO.15: 3 residues within 4Å:- Chain A: K.139, L.140
- Chain B: E.147
2 PLIP interactions:1 interactions with chain A, 1 interactions with chain B- Hydrogen bonds: A:K.139, B:E.147
EDO.19: 3 residues within 4Å:- Chain C: F.142, T.143
- Ligands: POP.5
No protein-ligand interaction detected (PLIP)EDO.20: 4 residues within 4Å:- Chain C: Q.104, A.105, K.107
- Ligands: CTN.18
No protein-ligand interaction detected (PLIP)- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Seattle Structural Genomics Center for Infectious Disease (SSGCID) et al., Crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Salmonella typhimurium bound to cytidine. To be Published
- Release Date
- 2011-09-14
- Peptides
- 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase: ABC
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
C
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.50 Å
- Oligo State
- homo-trimer
- Ligands
- 3 x ZN: ZINC ION(Non-covalent)
- 4 x MG: MAGNESIUM ION(Non-covalent)
- 3 x CTN: 4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE(Non-covalent)
- 1 x POP: PYROPHOSPHATE 2-(Non-covalent)
- 9 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Seattle Structural Genomics Center for Infectious Disease (SSGCID) et al., Crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Salmonella typhimurium bound to cytidine. To be Published
- Release Date
- 2011-09-14
- Peptides
- 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase: ABC
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
C