Ligand clusters for UniProt code Q38087

Ligand clusters for Q38087: DNA-directed DNA polymerase from Escherichia phage RB69

		Top 6 (of 33) ligand clusters Cluster 1. 26 ligand types 363 ligands Cluster 2. 7 ligand types 12 ligands Cluster 3. 1 ligand type 1 ligand Cluster 4. 2 ligand types 2 ligands Cluster 5. 4 ligand types 8 ligands Cluster 6. 1 ligand type 1 ligand
Representative protein: 3cfoA

Structures

PDB		Schematic diagram
3cfoA
1q9yA
5gnqA
4m45A
4fj8A
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Cluster 1 contains 26 ligand types (of which only 20 are listed. Click for all)

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Ligand		Description
		1. Ligand: TTP × 1 Thymidine-5'-Triphosphate PDB code: 1ig9(A).
		2. Ligand: DCP × 1 2'-Deoxycytidine-5'-Triphosphate PDB code: 1q9y(A).
		3. Ligand: DTP × 1 2'-Deoxyadenosine 5'-Triphosphate PDB code: 2ozs(A).
_Mg		4. Metal: _MG × 9 PDB codes: 2ozm(A), 2ozs(A), 3kd5(E), 3si6(A), 3snn(A), 3spy(A),
_Mn		5. Metal: _MN × 9 PDB codes: 3lds(A), 3sjj(A), 3sq0(A),
		6. Ligand: GOL × 1 glycerin Glycerol PDB code: 4khn(A).
		7. Ligand: PPF × 1 foscarnet Phosphonoformic acid PDB code: 3kd5(E).
		8. Ligand: N5P × 1 1-{2-Deoxy-5-O-[(R)-Hydroxy{[(r)-Hydroxy(phosphonooxy) phosphoryl]oxy}phosphoryl]-Beta-D-Erythro- Pentofuranosyl}-5-Nitro-1h-Indole PDB code: 2ozm(A).
		9. Ligand: DOC × 1 2',3'-Dideoxycytidine-5'-Monophosphate PDB code: 1q9x(A).
		10. Ligand: 3DR × 1 1',2'-Dideoxyribofuranose-5'-Phosphate PDB code: 1q9x(A).
_Ca		11. Metal: _CA × 230 PDB codes: 1clq(A), 1ig9(A), 1q9x(A), 1q9y(A), 3cfp(A), 3cfr(A), 3cq8(A), 3lzi(A), 3lzj(A), 3nae(A), 3nci(A), 3ndk(A), 3ne6(A), 3ngi(A), 3nhg(A), 3qei(A), 3qep(A), 3qer(A), 3qes(A), 3qet(A), 3qev(A), 3qew(A), 3qex(A), 3qnn(A), 3qno(A), 3rwu(A), 3s9h(A), 3scx(A), 3spz(A), 3sq1(A), 3sq2(A), 3sq4(A), 3sun(A), 3suo(A), 3sup(A), 3suq(A), 3uiq(A), 4dtj(A), 4dtm(A), 4dtn(A), 4dto(A), 4dtp(A), 4dtr(A), 4dts(A), 4dtu(A), 4dtx(A), 4du1(A), 4du3(A), 4du4(A), 4e3s(A), 4fj5(A), 4fj7(A), 4fj8(A), 4fj9(A), 4fjg(A), 4fjh(A), 4fji(A), 4fjj(A), 4fjk(A), 4fjl(A), 4fjm(A), 4fjn(A), 4fjx(A), 4fk0(A), 4fk2(A), 4fk4(A), 4i9q(A), 4j2a(A), 4j2b(A), 4j2d(A), 4j2e(A), 4khn(A), 4khq(A), 4khs(A), 4khu(A), 4khw(A), 4khy(A), 4ki4(A), 4ki6(A), 4m3r(A), 4m3t(A), 4m3u(A), 4m3w(A), 4m3x(A), 4m3y(A), 4m3z(A), 4m41(A), 4m42(A), 4m45(A), 5gnq(A).
		12. Ligand: TTP × 25 Thymidine-5'-Triphosphate PDB codes: 3cfp(A), 3cfr(A), 3cq8(A), 3ngi(A), 3nhg(A), 3qep(A), 3qet(A), 3sq2(A), 3sq4(A), 3sun(A), 3suo(A), 4dtj(A), 4dtx(A), 4fj9(A), 4fjj(A), 4fjn(A), 4fk2(A), 4j2a(A), 4j2d(A), 4khs(A), 4khu(A), 4khw(A), 4khy(A), 4ki4(A), 4ki6(A).
		13. Ligand: DCP × 15 2'-Deoxycytidine-5'-Triphosphate PDB codes: 3nci(A), 3ndk(A), 3ne6(A), 3qei(A), 3qev(A), 3snn(A), 3sup(A), 3suq(A), 4dtm(A), 4dto(A), 4dts(A), 4fj8(A), 4fji(A), 4fjm(A), 4fk0(A).
		14. Ligand: DTP × 14 2'-Deoxyadenosine 5'-Triphosphate PDB codes: 3lds(A), 3lzi(A), 3nae(A), 3qer(A), 3qew(A), 4dtn(A), 4dtr(A), 4du1(A), 4du3(A), 4du4(A), 4fj5(A), 4fjg(A), 4fjk(A), 4fjx(A).
		15. Ligand: ATP × 14 Adenosine-5'-Triphosphate PDB codes: 3qno(A), 3rwu(A), 4j2b(A), 4j2e(A), 4m3r(A), 4m3t(A), 4m3u(A), 4m3w(A), 4m3x(A), 4m3y(A), 4m3z(A), 4m41(A), 4m42(A), 4m45(A).
_Na		16. Metal: _NA × 10 PDB codes: 4i9q(A), 4khn(A), 4khq(A), 4khs(A), 4khu(A), 4khy(A), 4ki4(A).
		17. Ligand: DGT × 9 2'-Deoxyguanosine-5'-Triphosphate PDB codes: 3qes(A), 3qex(A), 3qnn(A), 4dtp(A), 4dtu(A), 4fj7(A), 4fjh(A), 4fjl(A), 4fk4(A).
		18. Ligand: DUP × 9 2'-Deoxyuridine 5'-Alpha,Beta-Imido-Triphosphate PDB codes: 3s9h(A), 3scx(A), 3si6(A), 3sjj(A), 3sq0(A), 3sq1(A), 3uiq(A), 4khq(A), 5gnq(A).
		19. Ligand: N5P × 1 1-{2-Deoxy-5-O-[(R)-Hydroxy{[(r)-Hydroxy(phosphonooxy) phosphoryl]oxy}phosphoryl]-Beta-D-Erythro- Pentofuranosyl}-5-Nitro-1h-Indole PDB code: 2oyq(C).
		20. Ligand: SO4 × 2 Sulfate ion PDB codes: 3tag(A), 4khn(A).
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Cluster 2 contains 7 ligand types

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Ligand		Description
		1. Ligand: GDP × 2 Guanosine-5'-Diphosphate PDB codes: 1clq(A), 2atq(A).
		2. Ligand: DGP × 1 2'-Deoxyguanosine-5'-Monophosphate PDB code: 1q9x(A).
		3. Ligand: 5GP × 1 Guanosine-5'-Monophosphate PDB code: 1waj(A).
		4. Ligand: GMP × 4 Guanosine PDB codes: 1ih7(A), 1waf(A), 3cfo(A), 4i9l(A).
		5. Ligand: 5GP × 1 Guanosine-5'-Monophosphate PDB code: 5gnq(A).
		6. Ligand: XG4 × 2 2'-Deoxy-5'-O-[(R)-Hydroxy{[(r)-Hydroxy(phosphonooxy) phosphoryl]amino}phosphoryl]guanosine PDB codes: 4i9q(A), 4khn(A).
		7. Ligand: N5P × 1 1-{2-Deoxy-5-O-[(R)-Hydroxy{[(r)-Hydroxy(phosphonooxy) phosphoryl]oxy}phosphoryl]-Beta-D-Erythro- Pentofuranosyl}-5-Nitro-1h-Indole PDB code: 2oyq(A).

Cluster 3 contains 1 ligand type

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Ligand		Description
		1. Ligand: N5P × 1 1-{2-Deoxy-5-O-[(R)-Hydroxy{[(r)-Hydroxy(phosphonooxy) phosphoryl]oxy}phosphoryl]-Beta-D-Erythro- Pentofuranosyl}-5-Nitro-1h-Indole PDB code: 2oyq(A).

Cluster 4 contains 2 ligand types

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Ligand		Description
		1. Ligand: GOL × 1 glycerin Glycerol PDB code: 3cq8(A).
		2. Ligand: SO4 × 1 Sulfate ion PDB code: 4khn(A).

Cluster 5 contains 4 ligand types

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Ligand		Description
_Na		1. Metal: _NA × 5 PDB codes: 4khq(A), 4khs(A), 4khw(A), 4khy(A), 4ki4(A).
		2. Ligand: PO4 × 1 Phosphate ion PDB code: 4ki6(A).
_Ca		3. Metal: _CA × 1 PDB code: 4j2d(A).
_Cl		4. Metal: _CL × 1 PDB code: 3cfp(A).

Cluster 6 contains 1 ligand type

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Ligand		Description
		1. Ligand: GOL × 1 glycerin Glycerol PDB code: 3cq8(A).