Ligand clusters for UniProt code P62617

Ligand clusters for P62617: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Escherichia coli (strain K12)

		4 ligand clusters Cluster 1. 13 ligand types 34 ligands Cluster 2. 10 ligand types 13 ligands Cluster 3. 4 ligand types 14 ligands Cluster 4. 1 ligand type 1 ligand
Representative protein: 3esjA

Structures

PDB		Schematic diagram
3esjA
2gzlA
3fbaA
1yqnA
1h48A
		more ...

Cluster 1 contains 13 ligand types

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Ligand		Description
		1. Ligand: C5P × 3 Cytidine-5'-Monophosphate PDB codes: 1h47(A), 1h48(A), 1jy8(A).
		2. Ligand: CDI × 2 2c-Methyl-D-Erythritol 2,4-Cyclodiphosphate PDB codes: 1h48(A), 1jy8(A).
		3. Ligand: SUD × 1 4-Diphosphocytidyl-2-C-Methyl-D-Erythritol 2-Phosphate PDB code: 1u43(A).
_Zn		4. Metal: _ZN × 15 PDB codes: 1gx1(A), 1h47(A), 1h48(A), 1jy8(A), 1u3l(A), 1u3p(A), 1u40(A), 1yqn(A), 2amt(A), 2gzl(A), 3elc(A), 3eor(A), 3ern(A), 3esj(A), 3fba(A).
_Mn		5. Metal: _MN × 2 PDB codes: 1knj(A), 1knk(A).
		6. Ligand: CDM × 1 4-Diphosphocytidyl-2-C-Methyl-D-Erythritol PDB code: 1u40(A).
		7. Ligand: CDP × 2 Cytidine-5'-Diphosphate PDB codes: 1u3l(A), 1yqn(A).
		8. Ligand: 1AA × 1 5'-O-[({[(2-{[(2-Aminophenyl)carbonyl]oxy}ethyl) oxy]phosphinato}oxy)phosphinato]cytidine PDB code: 2amt(A).
		9. Ligand: 2AA × 1 5'-O-{[({[2-({[5-(Dimethylamino)naphthalen-1- Yl]sulfonyl}amino)ethyl]oxy}phosphinato) oxy]phosphinato}cyt PDB code: 2gzl(A).
		10. Ligand: CDP × 1 Cytidine-5'-Diphosphate PDB code: 1gx1(A).
		11. Ligand: CAR × 2 Cytosine arabinose-5'-Phosphate PDB codes: 3ern(A),
_Na		12. Metal: _NA × 2 PDB codes: 3eor(A),
		13. Ligand: F01 × 1 4-Amino-1-[(2r,3r,4s,5r)-3,4-Dihydroxy-5- (Hydroxymethyl)oxolan-2-Yl]-5-Fluoro-Pyrimidin-2-One PDB code: 3elc(A).

Cluster 2 contains 10 ligand types

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Ligand		Description
		1. Ligand: C5P × 3 Cytidine-5'-Monophosphate PDB codes: 1h47(A), 1h48(A), 1knj(A).
		2. Ligand: CDI × 1 2c-Methyl-D-Erythritol 2,4-Cyclodiphosphate PDB code: 1h48(A).
_Mn		3. Metal: _MN × 2 PDB codes: 1gx1(A), 1yqn(A).
		4. Ligand: 1AA × 1 5'-O-[({[(2-{[(2-Aminophenyl)carbonyl]oxy}ethyl) oxy]phosphinato}oxy)phosphinato]cytidine PDB code: 2amt(A).
		5. Ligand: C6B × 1 [(2s,3s,4r,5s)-5-(4-Amino-2-Oxo-Pyrimidin-1-Yl)-4- Hydroxy-2-(Hydroxymethyl)oxolan-3- Yl] dihydrogen phosphate PDB code: 3fba(A).
		6. Ligand: CAR × 1 Cytosine arabinose-5'-Phosphate PDB code: 3ern(A).
		7. Ligand: CC7 × 1 4-Amino-1-[(2s,4ar,6r,7r,7as)-2,7-Dihydroxy-2- Oxidotetrahydro-4h-Furo[3,2- D][1,3,2]dioxaphosphinin- 6-Yl]pyrimidin-2(1h)-One PDB code: 3esj(A).
		8. Ligand: CDP × 1 Cytidine-5'-Diphosphate PDB code: 1gx1(A).
		9. Ligand: CFV × 1 [(2r)-1-(4-Amino-2-Oxo-Pyrimidin-1-Yl)-3-Hydroxy- Propan-2-Yl]oxymethylphosphonic acid PDB code: 3eor(A).
		10. Ligand: F01 × 1 4-Amino-1-[(2r,3r,4s,5r)-3,4-Dihydroxy-5- (Hydroxymethyl)oxolan-2-Yl]-5-Fluoro-Pyrimidin-2-One PDB code: 3elc(A).

Cluster 3 contains 4 ligand types

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Ligand		Description
_Mg		1. Metal: _MG × 1 PDB code: 3esj(A).
_Mn		2. Metal: _MN × 1 PDB code: 1h48(A).
		3. Ligand: GPP × 11 Geranyl diphosphate PDB codes: 1h47(A), 1h48(A), 1yqn(A), 2amt(A), 2gzl(A), 3elc(A), 3eor(A), 3ern(A), 3esj(A), 3fba(A).
		4. Ligand: SO4 × 1 Sulfate ion PDB code: 1gx1(A).

Cluster 4 contains 1 ligand type

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Ligand		Description
		1. Ligand: GOL × 1 glycerin Glycerol PDB code: 3fba(A).