Ligand clusters for UniProt code Q9NP87

Ligand clusters for Q9NP87: DNA-directed DNA/RNA polymerase mu from Homo sapiens

		Top 6 (of 33) ligand clusters Cluster 1. 31 ligand types 351 ligands Cluster 2. 4 ligand types 25 ligands Cluster 3. 3 ligand types 14 ligands Cluster 4. 6 ligand types 27 ligands Cluster 5. 3 ligand types 17 ligands Cluster 6. 2 ligand types 32 ligands
Representative protein: 4lzdA

Structures

PDB		Schematic diagram
4lzdA
6wicA
4yd1A
6ipkA
6ipnA
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Cluster 1 contains 31 ligand types (of which only 20 are listed. Click for all)

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Ligand		Description
_Mg		1. Metal: _MG × 68 PDB codes: 4m04(A), 4m0a(A), 4ycx(A), 4yd1(A), 5twp(A), 5twq(A), 5twr(A), 5tws(A), 5txz(A), 5tyb(A), 5tyc(A), 5tyd(A), 5tye(A), 5tyf(A), 5tyg(A), 5vz7(A), 5vz8(A), 5vz9(A), 5vza(A), 5vzb(A), 5vzc(A), 5vzd(A), 5vze(A), 5vzf(A), 5vzg(A), 5vzh(A), 5vzi(A), 6ipe(A), 6ipg(A), 6ipl(A), 6ipm(A), 6ipn(A), 6p1n(A), 6p1o(A), 6p1p(A), 6p1q(A), 6p1r(A), 6p1t(A), 6p1v(A), 6p1w(A),
_Mn		2. Metal: _MN × 41 PDB codes: 4m0a(A), 5twq(A), 5tyu(A), 5tyv(A), 5tyw(A), 5tyx(A), 5tyy(A), 5tyz(A), 5zlc(A), 6aec(A), 6aeh(A), 6ak5(A), 6ak6(A), 6akh(A), 6ipd(A), 6ipf(A), 6iph(A), 6ipi(A), 6ipj(A), 6ipk(A), 6p1o(A), 6p1s(A), 6p1u(A).
		3. Ligand: PPV × 19 pyrophosphoric acid Pyrophosphate PDB codes: 4m0a(A), 4yd2(A), 5twq(A), 5txz(A), 5tyb(A), 5tyc(A), 5tyd(A), 5tye(A), 5tyu(A), 5tyv(A), 5tyw(A), 5tyx(A), 5tyy(A), 6ipf(A), 6p1o(A), 6p1q(A), 6p1u(A), 6wid(A), 6wie(A).
		4. Ligand: GOA × 6 glycolic acid Glycolic acid PDB codes: 5tws(A), 5tyf(A), 5tyg(A), 5tyz(A), 5vze(A), 5vzh(A).
		5. Ligand: GOL × 1 glycerin Glycerol PDB code: 4lzg(A).
__K		6. Metal: __K × 1 PDB code: 6p1m(A).
_Na		7. Metal: _NA × 64 PDB codes: 4lzd(A), 4lzg(A), 4m04(A), 4yd1(A), 4yd2(A), 5twp(A), 5twq(A), 5twr(A), 5tws(A), 5txx(A), 5txz(A), 5tyb(A), 5tyc(A), 5tyd(A), 5tye(A), 5tyf(A), 5tyg(A), 5tyu(A), 5tyv(A), 5tyw(A), 5tyx(A), 5tyy(A), 5tyz(A), 5vz7(A), 5vz8(A), 5vz9(A), 5vza(A), 5vzb(A), 5vzc(A), 5vzd(A), 5vze(A), 5vzf(A), 5vzg(A), 5vzh(A), 5vzi(A), 6ak8(A), 6ak9(A), 6akh(A), 6ipd(A), 6ipe(A), 6ipf(A), 6ipg(A), 6p1n(A), 6p1o(A), 6p1p(A), 6p1q(A), 6p1r(A), 6p1s(A), 6p1t(A), 6p1u(A), 6p1v(A), 6p1w(A).
		8. Ligand: EDO × 46 1,2-Ethanediol PDB codes: 4m04(A), 4m0a(A), 4yd1(A), 5twq(A), 5tws(A), 5txx(A), 5txz(A), 5tyb(A), 5tyc(A), 5tyd(A), 5tye(A), 5tyf(A), 5tyg(A), 5tyu(A), 5tyv(A), 5tyw(A), 5tyx(A), 5tyy(A), 5tyz(A), 5vz8(A), 5vz9(A), 5vzb(A), 5vzc(A), 5vzd(A), 5vzg(A), 5vzi(A), 6ak8(A), 6ak9(A), 6akh(A), 6ipd(A), 6ipe(A), 6ipf(A), 6ipg(A), 6p1m(A), 6p1o(A), 6p1p(A), 6p1s(A), 6p1t(A), 6p1u(A), 6p1v(A).
_Cl		9. Metal: _CL × 22 PDB codes: 4lzd(A), 4lzg(A), 4yd1(A), 5twq(A), 5twr(A), 5tws(A), 5vz7(A), 5vz9(A), 5vzc(A), 5vzg(A), 6ak8(A), 6p1n(A), 6p1o(A), 6p1p(A), 6p1q(A), 6p1r(A), 6p1s(A), 6p1t(A), 6p1u(A), 6p1v(A), 6p1w(A).
		10. Ligand: SO4 × 15 Sulfate ion PDB codes: 6aec(A), 6aeh(A), 6ak5(A), 6ak6(A), 6ipk(A), 6ipl(A), 6ipm(A), 6ipn(A), 6wie(A).
		11. Ligand: TTP × 15 Thymidine-5'-Triphosphate PDB codes: 5txx(A), 5txz(A), 5tyb(A), 5tyc(A), 5tyd(A), 5tyu(A), 5tyv(A), 5tyw(A), 5vz9(A), 5vzc(A), 5vzf(A), 5vzi(A), 6ipj(A).
_Ca		12. Metal: _CA × 10 PDB codes: 5txx(A), 5txz(A), 5tyb(A), 5tyc(A), 5tyu(A), 6ak8(A), 6ak9(A),
		13. Ligand: 2KH × 6 5'-O-[(S)-Hydroxy{[(s)-Hydroxy(phosphonooxy) phosphoryl]amino}phosphoryl]uridine PDB codes: 5twp(A), 5twr(A), 5vz7(A), 5vza(A), 5vzd(A), 5vzg(A).
		14. Ligand: DUP × 5 2'-Deoxyuridine 5'-Alpha,Beta-Imido-Triphosphate PDB codes: 4m04(A), 4yd1(A), 6akh(A), 6wic(A), 6wid(A).
		15. Ligand: UTP × 5 Uridine 5'-Triphosphate PDB codes: 5vz8(A), 5vzb(A), 5vze(A), 5vzh(A), 6aeh(A).
		16. Ligand: 8DG × 3 8-Oxo-2'-Deoxyguanosine-5'-Triphosphate PDB codes: 6ak8(A), 6ak9(A), 6ipk(A).
		17. Ligand: ATP × 3 Adenosine-5'-Triphosphate PDB codes: 6aec(A), 6p1o(A), 6p1s(A).
		18. Ligand: 0KX × 2 2'-Deoxy-5'-O-[(R)-Hydroxy{[(r)-Hydroxy(phosphonooxy) phosphoryl]amino}phosphoryl]cytidine PDB codes: 6p1p(A), 6p1v(A).
		19. Ligand: 2TM × 2 5'-O-[(S)-Hydroxy{[(s)-Hydroxy(phosphonooxy) phosphoryl]methyl}phosphoryl]cytidine PDB codes: 6p1t(A), 6p1w(A).
		20. Ligand: CTP × 2 Cytidine-5'-Triphosphate PDB codes: 6ak6(A), 6p1u(A).
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Cluster 2 contains 4 ligand types

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Ligand		Description
		1. Ligand: SO4 × 11 Sulfate ion PDB codes: 5zlc(A), 6aec(A), 6aeh(A), 6ak5(A), 6ak6(A), 6iph(A), 6ipi(A), 6ipj(A), 6ipl(A), 6ipm(A), 6ipn(A).
_Cl		2. Metal: _CL × 11 PDB codes: 4lzg(A), 4m04(A), 4yd1(A), 4yd2(A), 5twr(A), 6p1n(A), 6p1o(A), 6p1q(A), 6p1s(A), 6p1t(A), 6p1u(A).
		3. Ligand: EDO × 2 1,2-Ethanediol PDB codes: 5txz(A), 6p1n(A).
		4. Ligand: EPE × 1 4-(2-Hydroxyethyl)-1-Piperazine ethanesulfonic acid PDB code: 6ipf(A).

Cluster 3 contains 3 ligand types

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Ligand		Description
		1. Ligand: SO4 × 10 Sulfate ion PDB codes: 5zlc(A), 6aec(A), 6aeh(A), 6ak5(A), 6ak6(A), 6ipi(A), 6ipj(A), 6ipl(A), 6ipm(A), 6ipn(A).
		2. Ligand: 1PE × 3 Pentaethylene glycol PDB codes: 6wic(A), 6wid(A), 6wie(A).
		3. Ligand: EDO × 1 1,2-Ethanediol PDB code: 5tyu(A).

Cluster 4 contains 6 ligand types

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Ligand		Description
		1. Ligand: GOL × 5 glycerin Glycerol PDB codes: 4ycx(A), 4yd1(A), 5vzc(A), 6wic(A), 6wie(A).
_Mn		2. Metal: _MN × 5 PDB codes: 5tyv(A), 5tyw(A), 5tyx(A), 5tyy(A), 5tyz(A).
		3. Ligand: EDO × 11 1,2-Ethanediol PDB codes: 4m04(A), 5txz(A), 5tyb(A), 5tyd(A), 5tye(A), 5vzc(A), 5vzi(A), 6ak8(A), 6ak9(A), 6akh(A), 6p1t(A).
		4. Ligand: PEG × 3 Di(hydroxyethyl)ether PDB codes: 6wic(A), 6wid(A), 6wie(A).
_Na		5. Metal: _NA × 2 PDB codes: 6ipd(A), 6ipf(A).
_Cl		6. Metal: _CL × 1 PDB code: 6p1r(A).

Cluster 5 contains 3 ligand types

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Ligand		Description
		1. Ligand: GOL × 1 glycerin Glycerol PDB code: 4ycx(A).
		2. Ligand: EDO × 15 1,2-Ethanediol PDB codes: 4m0a(A), 5twp(A), 5twq(A), 5txz(A), 5tyb(A), 5tyd(A), 5tye(A), 5tyf(A), 5tyg(A), 5tyu(A), 5tyw(A), 5tyz(A), 5vz8(A), 6p1m(A), 6p1n(A).
		3. Ligand: SO4 × 1 Sulfate ion PDB code: 6iph(A).

Cluster 6 contains 2 ligand types

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Ligand		Description
		1. Ligand: EDO × 31 1,2-Ethanediol PDB codes: 4m0a(A), 4yd1(A), 5twp(A), 5twq(A), 5twr(A), 5tyd(A), 5tyg(A), 5tyv(A), 5tyw(A), 5tyx(A), 5tyz(A), 5vz7(A), 5vz8(A), 5vz9(A), 5vza(A), 5vzb(A), 5vzc(A), 5vzd(A), 5vze(A), 5vzf(A), 5vzg(A), 5vzh(A), 5vzi(A), 6ak8(A), 6ak9(A), 6akh(A), 6ipd(A), 6ipe(A), 6ipf(A), 6ipg(A), 6p1v(A).
		2. Ligand: SO4 × 1 Sulfate ion PDB code: 6ipk(A).