Ligand clusters for UniProt code P33590

Ligand clusters for P33590: Nickel-binding periplasmic protein from Escherichia coli (strain K12)

		Top 6 (of 61) ligand clusters Cluster 1. 20 ligand types 93 ligands Cluster 2. 3 ligand types 12 ligands Cluster 3. 3 ligand types 20 ligands Cluster 4. 3 ligand types 16 ligands Cluster 5. 3 ligand types 18 ligands Cluster 6. 3 ligand types 5 ligands
Representative protein: 1zlqA

Structures

PDB		Schematic diagram
1zlqA
2nooA
4i8cA
3mw0A
5on0A
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Cluster 1 contains 20 ligand types

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Ligand		Description
		1. Ligand: GOL × 37 glycerin Glycerol PDB codes: 3mvw(A), 3mvx(A), 3mvy(A), 3mvz(A), 3qim(A), 4dcx(A), 4dcy(A), 4i8c(A), 4i9d(A), 5l8d(A), 5mwu(A), 5on0(A), 5on1(A), 5on5(A), 5on8(A), 5on9(A), 6r4q(A), 7a0c(A),
		2. Ligand: EDT × 4 edetic acid {[-(Bis-Carboxymethyl-Amino)-Ethyl]-Carboxymethyl- Amino}-Acetic acid PDB codes: 1zlq(A), 5l8d(A), 5mwu(A), 6r4q(A).
		3. Ligand: ACT × 18 Acetate ion PDB codes: 1zlq(A), 3dp8(A), 3mvx(A), 3mvz(A), 3mz9(A), 3mzb(A), 3qim(A), 4dcy(A), 4i8c(A), 4i9d(A), 5l8d(A), 5mwu(A), 5on5(A), 5on9(A), 6r4q(A), 7a0c(A).
		4. Ligand: 9YH × 4 2-[2-[2-Hydroxy-2-Oxoethyl-[(3-Methoxy-2-Oxidanyl- Phenyl)methyl]amino]ethyl-[(2- Methylsulfanylphenyl) methyl]amino]ethanoic acid PDB codes: 5on0(A), 5on5(A), 5on8(A), 5on9(A).
		5. Ligand: DTD × 4 Dithiane diol PDB codes: 3mw0(A), 3mz9(A), 3mzb(A), 5on1(A).
_Cl		6. Metal: _CL × 4 PDB codes: 1zlq(A), 3dp8(A), 3mzb(A),
		7. Ligand: BHZ × 3 2-[2-[Carboxymethyl(phenylmethyl)amino]ethyl-[(2- Hydroxyphenyl)methyl]amino]ethanoic acid PDB codes: 3mvw(A), 3mvx(A), 3mvy(A).
		8. Ligand: 9YK × 2 2-[2-[[2,3-Bis(oxidanyl)phenyl]methyl-(2-Hydroxy-2- Oxoethyl)amino]ethyl-[(2- Methylsulfanylphenyl) methyl]amino]ethanoic acid PDB codes: 5on1(A), 5on4(A).
		9. Ligand: BHN × 2 2-[2-[Carboxymethyl-[(2-Hydroxyphenyl) methyl]amino]ethyl-[(2- Hydroxyphenyl) methyl]amino]ethanoic acid PDB codes: 3mvz(A), 3mz9(A).
		10. Ligand: BHR × 2 2-[2-[Carboxymethyl-[(2-Hydroxyphenyl) methyl]amino]ethyl-[(2,3- Dihydroxyphenyl) methyl]amino]ethanoic acid PDB codes: 3mw0(A), 3mzb(A).
		11. Ligand: HCT × 2 (2r)-Butane-1,2,4-Tricarboxylic acid PDB codes: 3dp8(A), 3e3k(A).
		12. Ligand: HIS × 2 PDB codes: 4i8c(A),
		13. Ligand: SO4 × 2 Sulfate ion PDB codes: 3qim(A),
		14. Ligand: DTT × 1 2,3-Dihydroxy-1,4-Dithiobutane PDB code: 5on9(A).
		15. Ligand: DTU × 1 (2r,3s)-1,4-Dimercaptobutane-2,3-Diol PDB code: 3mvx(A).
		16. Ligand: L2D × 1 {2,2'-[(1r,2r)-Cyclohexane-1,2-Diylbis{[(pyridin-2-Yl- Kappan)methyl]imino-Kappan}]diacetato- Kappao(2-)}Iron PDB code: 4dcx(A).
		17. Ligand: L2M-UNX × 1 L2M={(R)-N-[(1s,2s)-2-{Methyl[(pyridin-2-Yl-Kappan) methyl]amino-Kappan}cyclohexyl]-N-[(Pyridin-2-Yl- Kappan)methyl]glycinato-Kappa~2~n,O}iron(2+), UNX=Unknown atom or ion. PDB code: 4dcy(A).
		18. Ligand: L4D × 1 {(S)-N-(2-{Methyl[(pyridin-2-Yl-Kappan)methyl]amino- Kappan}ethyl)-N-[(Pyridin-2-Yl- Kappan) methyl]glycinato-Kappa~2~n,O}iron(2+) PDB code: 4i9d(A).
		19. Ligand: QTT × 1 2-[[(1~{s},2~{s})-2-[Methyl-[(6-Methylpyridin-2-Yl) methyl]amino]cyclohexyl]-[(6-Methylpyridin-2- Yl) methyl]amino]ethanoic acid PDB code: 7a0c(A).
_Ni		20. Metal: _NI × 1 PDB code: 4i8c(A).
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Cluster 2 contains 3 ligand types

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Ligand		Description
		1. Ligand: GOL × 10 glycerin Glycerol PDB codes: 3mvx(A), 3mvz(A), 4dcx(A), 4i9d(A), 5on0(A), 5on1(A), 5on5(A), 5on9(A), 6r4q(A).
		2. Ligand: ACT × 1 Acetate ion PDB code: 3mvy(A).
		3. Ligand: DTT × 1 2,3-Dihydroxy-1,4-Dithiobutane PDB code: 1zlq(A).

Cluster 3 contains 3 ligand types

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Ligand		Description
		1. Ligand: GOL × 3 glycerin Glycerol PDB codes: 3mz9(A), 3mzb(A), 5on9(A).
		2. Ligand: ACT × 16 Acetate ion PDB codes: 1zlq(A), 3mvw(A), 3mvx(A), 3mvy(A), 3mvz(A), 3mz9(A), 3mzb(A), 3qim(A), 4dcy(A), 4i9d(A), 5l8d(A), 5mwu(A), 5on0(A), 5on1(A), 5on8(A), 7a0c(A).
		3. Ligand: SO4 × 1 Sulfate ion PDB code: 4dcx(A).

Cluster 4 contains 3 ligand types

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Ligand		Description
		1. Ligand: GOL × 7 glycerin Glycerol PDB codes: 1zlq(A), 3mvy(A), 3mvz(A), 3mz9(A), 3mzb(A), 3qim(A), 4dcy(A).
		2. Ligand: ACT × 8 Acetate ion PDB codes: 4dcx(A), 4i8c(A), 5l8d(A), 5mwu(A), 5on5(A), 5on8(A), 5on9(A), 6r4q(A).
		3. Ligand: SO4 × 1 Sulfate ion PDB code: 4i9d(A).

Cluster 5 contains 3 ligand types

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Ligand		Description
		1. Ligand: GOL × 9 glycerin Glycerol PDB codes: 1zlq(A), 3mvy(A), 3mvz(A), 4dcy(A), 4i8c(A), 5on1(A), 5on5(A), 6r4q(A).
		2. Ligand: ACT × 7 Acetate ion PDB codes: 4dcx(A), 4dcy(A), 4i9d(A), 5l8d(A), 5mwu(A), 5on0(A), 5on8(A).
		3. Ligand: SO4 × 2 Sulfate ion PDB codes: 3dp8(A), 3e3k(A).

Cluster 6 contains 3 ligand types

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Ligand		Description
		1. Ligand: GOL × 3 glycerin Glycerol PDB codes: 5on0(A), 5on4(A), 5on9(A).
		2. Ligand: DTU × 1 (2r,3s)-1,4-Dimercaptobutane-2,3-Diol PDB code: 3mvx(A).
_Ni		3. Metal: _NI × 1 PDB code: 2noo(A).