Ligand clusters for UniProt code P20906

Ligand clusters for P20906: Benzoylformate decarboxylase from Pseudomonas putida

		Top 6 (of 30) ligand clusters Cluster 1. 9 ligand types 15 ligands Cluster 2. 12 ligand types 83 ligands Cluster 3. 2 ligand types 2 ligands Cluster 4. 2 ligand types 15 ligands Cluster 5. 2 ligand types 6 ligands Cluster 6. 3 ligand types 3 ligands
Representative protein: 2v3wA

Structures

PDB		Schematic diagram
2v3wA
6m2yA
3fznA
1bfdA
4jubA
		more ...

Cluster 1 contains 9 ligand types

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Ligand		Description
		1. Ligand: TPP × 1 Thiamine diphosphate PDB code: 2v3w(A).
		2. Ligand: TDP × 2 cocarboxylase Thiamin diphosphate PDB codes: 1mcz(A), 5dei(A).
		3. Ligand: RMN × 1 (R)-Mandelic acid PDB code: 1mcz(A).
		4. Ligand: TPP × 5 Thiamine diphosphate PDB codes: 4jub(A), 4juc(A), 4juf(A), 4k9o(A), 4k9p(A).
		5. Ligand: 8PA × 2 3-[(4-Amino-2-Methylpyrimidin-5-Yl)methyl]-5-(2-{[(S)- Hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)- 2-[(1s,2e)- 1-Hydroxy-3-Pyridin-3-Ylprop-2-En-1-Yl]-4-Methyl-1,3- Thiazol-3-Ium PDB codes: 3f6b(X), 3f6e(X).
		6. Ligand: BCT × 1 Bicarbonate ion PDB code: 5dei(A).
		7. Ligand: D7K × 1 3-[(4-Amino-2-Methylpyrimidin-5-Yl)methyl]-2-{(S)- Hydroxy[(r)- Hydroxy(methoxy)phosphoryl]phenylmethyl}- 5-(2-{[(R)-Hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)- 4-Methyl-1,3-Thiazol-3-Ium PDB code: 3fzn(A).
		8. Ligand: SO4 × 1 Sulfate ion PDB code: 2v3w(A).
		9. Ligand: TZD × 1 2-{3-[(4-Amino-2-Methylpyrimidin-5-Yl)methyl]-4-Methyl- 2-Oxo-2,3-Dihydro-1,3-Thiazol-5- Yl}ethyl trihydrogen diphosphate PDB code: 4k9n(A).

Cluster 2 contains 12 ligand types

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Ligand		Description
		1. Ligand: TPP × 2 Thiamine diphosphate PDB codes: 1bfd(A), 2v3w(A).
		2. Ligand: TDP × 4 cocarboxylase Thiamin diphosphate PDB codes: 1mcz(A), 2fwn(A), 5dei(A), 5dgd(A).
_Mg		3. Metal: _MG × 4 PDB codes: 1mcz(A), 2v3w(A), 3fzn(A), 4k9n(A).
		4. Ligand: RMN × 1 (R)-Mandelic acid PDB code: 1mcz(A).
		5. Ligand: TZD × 3 2-{3-[(4-Amino-2-Methylpyrimidin-5-Yl)methyl]-4-Methyl- 2-Oxo-2,3-Dihydro-1,3-Thiazol-5- Yl}ethyl trihydrogen diphosphate PDB codes: 1pi3(A), 1po7(A), 2fn3(A).
_Ca		6. Metal: _CA × 34 PDB codes: 1pi3(A), 1po7(A), 1yno(A), 2fn3(A), 2fwn(A), 3fsj(X), 4gg1(A), 4gm0(A), 4gm1(A), 4gm4(A), 4gp9(A), 4gpe(A), 4jd5(A), 4ju8(A), 4ju9(A), 4jua(A), 4jub(A), 4juc(A), 4jud(X), 4juf(A), 4k9k(A), 4k9l(A), 4k9m(A), 4k9o(A), 4k9p(A), 4mpj(A), 4mpp(A), 4mpr(A), 4mq5(A), 4mzx(A), 4qel(A), 5dei(A), 5dgd(A), 5dgt(A).
		7. Ligand: TZD × 18 2-{3-[(4-Amino-2-Methylpyrimidin-5-Yl)methyl]-4-Methyl- 2-Oxo-2,3-Dihydro-1,3-Thiazol-5- Yl}ethyl trihydrogen diphosphate PDB codes: 1yno(A), 4gg1(A), 4gm0(A), 4gm1(A), 4gm4(A), 4gp9(A), 4gpe(A), 4jd5(A), 4ju8(A), 4ju9(A), 4jua(A), 4jud(X), 4k9l(A), 4k9n(A), 4mpp(A), 4mzx(A), 4qel(A), 5dgt(A).
		8. Ligand: TPP × 12 Thiamine diphosphate PDB codes: 4jub(A), 4juc(A), 4juf(A), 4k9k(A), 4k9m(A), 4k9o(A), 4k9p(A), 4mpj(A), 4mpr(A), 4mq5(A), 6m2y(A), 6m2z(A).
		9. Ligand: D7K × 2 3-[(4-Amino-2-Methylpyrimidin-5-Yl)methyl]-2-{(S)- Hydroxy[(r)- Hydroxy(methoxy)phosphoryl]phenylmethyl}- 5-(2-{[(R)-Hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)- 4-Methyl-1,3-Thiazol-3-Ium PDB codes: 3fsj(X), 3fzn(A).
		10. Ligand: BCT × 1 Bicarbonate ion PDB code: 5dei(A).
		11. Ligand: EDO × 1 1,2-Ethanediol PDB code: 4k9l(A).
		12. Ligand: SO4 × 1 Sulfate ion PDB code: 2v3w(A).

Cluster 3 contains 2 ligand types

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Ligand		Description
		1. Ligand: GOL × 1 glycerin Glycerol PDB code: 4jud(X).
		2. Ligand: EDO × 1 1,2-Ethanediol PDB code: 4k9l(A).

Cluster 4 contains 2 ligand types

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Ligand		Description
		1. Ligand: GOL × 1 glycerin Glycerol PDB code: 4k9p(A).
_Ca		2. Metal: _CA × 14 PDB codes: 1pi3(A), 1po7(A), 1yno(A), 2fn3(A), 2fwn(A), 4gg1(A), 4gp9(A), 4mpj(A), 4mpp(A), 4mpr(A), 4mq5(A), 4qel(A), 5dgd(A), 5dgt(A).

Cluster 5 contains 2 ligand types

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Ligand		Description
		1. Ligand: GOL × 1 glycerin Glycerol PDB code: 4k9p(A).
_Ca		2. Metal: _CA × 5 PDB codes: 4gm0(A), 4gm1(A), 4gm4(A), 4gpe(A), 4jd5(A).

Cluster 6 contains 3 ligand types

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Ligand		Description
_Mg		1. Metal: _MG × 1 PDB code: 4jub(A).
		2. Ligand: EDO × 1 1,2-Ethanediol PDB code: 4k9l(A).
_Cl		3. Metal: _CL × 1 PDB code: 3fzn(A).