Ligand clusters for UniProt code P19821

Ligand clusters for P19821: DNA polymerase I, thermostable from Thermus aquaticus

		Top 6 (of 52) ligand clusters Cluster 1. 42 ligand types 174 ligands Cluster 2. 2 ligand types 2 ligands Cluster 3. 6 ligand types 56 ligands Cluster 4. 6 ligand types 8 ligands Cluster 5. 4 ligand types 11 ligands Cluster 6. 6 ligand types 8 ligands
Representative protein: 1taqA

Structures

PDB		Schematic diagram
1taqA
1tauA
4c8lA
4c8nA
5ktqA
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Cluster 1 contains 42 ligand types (of which only 20 are listed. Click for all)

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Ligand		Description
		1. Ligand: DCP × 1 2'-Deoxycytidine-5'-Triphosphate PDB code: 5ktq(A).
		2. Ligand: TTP × 1 Thymidine-5'-Triphosphate PDB code: 1qtm(A).
_Mg		3. Metal: _MG × 76 PDB codes: 1qss(A), 1qsy(A), 1qtm(A), 2ktq(A), 3ktq(A), 3lwl(A), 3m8r(A), 3m8s(A), 3ojs(A), 3oju(A), 3po5(A), 3py8(A), 3rtv(A), 3sv3(A), 3t3f(A), 4bwj(A), 4df4(A), 4df8(A), 4dfj(A), 4dfk(A), 4dfm(A), 4dfp(A), 4dle(A), 4dlg(A), 4elt(A), 4elu(A), 4elv(A), 4n56(A), 4n5s(A), 4xiu(A), 5e41(A), 5nkl(A), 5o7t(A), 5szt(A), 5w6k(A), 5ytc(A), 5ytd(A), 5yte(A), 5ytf(A), 5ytg(A), 5yth(A), 5z3n(A), 6q4u(A), 6q4v(A).
_Mn		4. Metal: _MN × 21 PDB codes: 3py8(A), 4dle(A), 4n5s(A), 5oxj(A), 6fbc(A), 6fbd(A), 6fbe(A), 6fbf(A), 6fbg(A), 6fbh(A), 6fbi(A), 6q4u(A), 6q4v(A).
		5. Ligand: GOL × 9 glycerin Glycerol PDB codes: 3lwm(A), 3rr7(A), 4c8l(A), 4c8m(A), 4elt(A), 4elu(A), 5o7t(A).
		6. Ligand: DG3 × 1 2'-3'-Dideoxyguanosine-5'-Triphosphate PDB code: 1qss(A).
		7. Ligand: DCT × 8 2',3'-Dideoxycytidine 5'-Triphosphate PDB codes: 2ktq(A), 3ktq(A), 3py8(A), 4bwj(A), 4bwm(A), 4dle(A), 4dlg(A), 4n5s(A).
		8. Ligand: XG4 × 7 2'-Deoxy-5'-O-[(R)-Hydroxy{[(r)-Hydroxy(phosphonooxy) phosphoryl]amino}phosphoryl]guanosine PDB codes: 6fbc(A), 6fbd(A), 6fbe(A), 6fbf(A), 6fbg(A), 6fbh(A), 6fbi(A).
		9. Ligand: DDS × 5 2',3'-Dideoxyadenosine triphosphate PDB codes: 1qsy(A), 3lwl(A), 3lwm(A), 3po4(A), 3po5(A).
		10. Ligand: DGT × 5 2'-Deoxyguanosine-5'-Triphosphate PDB codes: 5ytd(A), 5ytf(A), 5ytg(A), 5yth(A), 5z3n(A).
		11. Ligand: EDO × 4 1,2-Ethanediol PDB codes: 4df8(A), 4dfk(A), 4dfm(A), 4dfp(A).
		12. Ligand: DCP × 2 2'-Deoxycytidine-5'-Triphosphate PDB codes: 3rtv(A), 5o7t(A).
		13. Ligand: DG3 × 2 2'-3'-Dideoxyguanosine-5'-Triphosphate PDB codes: 3rr8(A), 3rrg(A).
		14. Ligand: DTP × 3 2'-Deoxyadenosine 5'-Triphosphate PDB codes: 5ytc(A), 5yte(A), 6q4v(A).
		15. Ligand: SO4 × 2 Sulfate ion PDB codes: 4c8l(A), 4c8o(A).
		16. Ligand: TTP × 1 Thymidine-5'-Triphosphate PDB code: 3rrh(A).
		17. Ligand: 0KL × 1 5-(5-Aminopent-1-Yn-1-Yl)-2'-Deoxyuridine 5'- (Tetrahydrogen triphosphate) PDB code: 4dfj(A).
		18. Ligand: 0L3 × 1 7-{2-Deoxy-5-O-[(S)-Hydroxy{[(s)-Hydroxy(phosphonooxy) phosphoryl]oxy}phosphoryl]-Beta-D-Erythro- Pentofuranosyl}-5-{5-[(10-Hydroxydecanoyl)amino]pent- 1-Yn-1-Yl}-7h-Pyrrolo[2,3-D]pyrimidin-4- Amine PDB code: 4df4(A).
		19. Ligand: 0L4 × 1 5-(5-Aminopent-1-Yn-1-Yl)-7-{2-Deoxy-5-O-[(S)- Hydroxy{[(s)- Hydroxy(phosphonooxy) phosphoryl]oxy}phosphoryl]-Beta-D-Erythro- Pentofuranosyl}-7h-Pyrrolo[2,3- D]pyrimidin-4-Amine PDB code: 4df8(A).
		20. Ligand: 0L5 × 1 2'-Deoxy-5-{5-[(10-Hydroxydecanoyl)amino]pent-1-Yn-1- Yl}uridine 5'-(Tetrahydrogen triphosphate) PDB code: 4dfk(A).
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Cluster 2 contains 2 ligand types

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Ligand		Description
		1. Ligand: 5SI × 1 2-{2-Deoxy-5-O-[(R)-Hydroxy{[(r)-Hydroxy(phosphonooxy) phosphoryl]oxy}phosphoryl]-Beta-D-Erythro- Pentofuranosyl}-6-Methylisoquinoline-1(2h)-Thione PDB code: 3sv3(A).
		2. Ligand: EDO × 1 1,2-Ethanediol PDB code: 4dfp(A).

Cluster 3 contains 6 ligand types

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Ligand		Description
		1. Ligand: GOL × 34 glycerin Glycerol PDB codes: 3lwl(A), 3lwm(A), 3m8r(A), 3ojs(A), 3oju(A), 3py8(A), 3rr8(A), 3rrg(A), 3rrh(A), 3rtv(A), 3sv3(A), 3syz(A), 3sz2(A), 3t3f(A), 4dle(A), 4dlg(A), 4elt(A), 4elu(A), 4elv(A), 4n56(A), 5e41(A), 5szt(A), 5yte(A), 5yth(A), 5z3n(A).
		2. Ligand: ACT × 8 Acetate ion PDB codes: 3lwl(A), 3lwm(A), 3m8r(A), 3m8s(A), 3rrg(A), 4elt(A), 5oxj(A), 5szt(A).
		3. Ligand: EDO × 6 1,2-Ethanediol PDB codes: 4df4(A), 4dfj(A), 4dfk(A), 4dfm(A), 6fbh(A), 6q4u(A).
		4. Ligand: PGE × 5 Triethylene glycol PDB codes: 3ojs(A), 3oju(A), 3po5(A), 3rrh(A).
		5. Ligand: 15P × 2 Polyethylene glycol (n=34) PDB codes: 3m8r(A), 3m8s(A).
		6. Ligand: SO4 × 1 Sulfate ion PDB code: 4c8o(A).

Cluster 4 contains 6 ligand types

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Ligand		Description
_Mg		1. Metal: _MG × 3 PDB codes: 5oxj(A), 6fbc(A), 6fbe(A).
		2. Ligand: GOL × 1 glycerin Glycerol PDB code: 5z3n(A).
_Mn		3. Metal: _MN × 1 PDB code: 3py8(A).
		4. Ligand: 15P × 1 Polyethylene glycol (n=34) PDB code: 3m8r(A).
		5. Ligand: ACT × 1 Acetate ion PDB code: 3rtv(A).
		6. Ligand: PGE × 1 Triethylene glycol PDB code: 3ojs(A).

Cluster 5 contains 4 ligand types

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Ligand		Description
		1. Ligand: GOL × 4 glycerin Glycerol PDB codes: 3lwl(A), 3oju(A), 3t3f(A), 4elt(A).
		2. Ligand: EDO × 4 1,2-Ethanediol PDB codes: 4df8(A), 4dfm(A), 4dfp(A), 6fbg(A).
_Na		3. Metal: _NA × 2 PDB codes: 3lwl(A), 3lwm(A).
		4. Ligand: EPE × 1 4-(2-Hydroxyethyl)-1-Piperazine ethanesulfonic acid PDB code: 4n5s(A).

Cluster 6 contains 6 ligand types

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Ligand		Description
		1. Ligand: GOL × 1 glycerin Glycerol PDB code: 3lwm(A).
		2. Ligand: ACT × 2 Acetate ion PDB codes: 4dlg(A), 4n5s(A).
		3. Ligand: EDO × 2 1,2-Ethanediol PDB codes: 4elv(A), 6fbg(A).
		4. Ligand: PGE × 1 Triethylene glycol PDB code: 3ojs(A).
		5. Ligand: SO4 × 1 Sulfate ion PDB code: 4c8o(A).
_Cl		6. Metal: _CL × 1 PDB code: 4c8o(A).