Ligand clusters for UniProt code D0VWU9

Ligand clusters for D0VWU9: DNA polymerase from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)

		Top 6 (of 9) ligand clusters Cluster 1. 6 ligand types 8 ligands Cluster 2. 2 ligand types 3 ligands Cluster 3. 1 ligand type 1 ligand Cluster 4. 1 ligand type 1 ligand Cluster 5. 1 ligand type 1 ligand Cluster 6. 1 ligand type 1 ligand
Representative protein: 5vu8A

Structures

PDB		Schematic diagram
5vu8A
6wyaA
5vu7A
1wn7A
6wybA

Cluster 1 contains 6 ligand types

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Ligand		Description
_Mg		1. Metal: _MG × 3 PDB codes: 5vu8(A), 6wya(A).
		2. Ligand: GOL × 1 glycerin Glycerol PDB code: 1wn7(A).
		3. Ligand: 9O7 × 1 [(3~{s},4~{r},5~{r})-5-(6-Aminopurin-9-Yl)-4-Oxidanyl- Oxolan-3- Yl] [oxidanyl(phosphonooxy)phosphoryl] hydrogen phosphate PDB code: 5vu8(A).
		4. Ligand: DZ4 × 1 2'-Deoxy-5'-O-[(R)-Hydroxy{[(r)-Hydroxy(phosphonooxy) phosphoryl]amino}phosphoryl]adenosine PDB code: 6wya(A).
		5. Ligand: FA2 × 1 5-(6-Amino-9h-Purin-9-Yl)-4-Hydroxytetrahydrofuran-3-Yl dihydrogen phosphate PDB code: 5vu7(A).
		6. Ligand: SO4 × 1 Sulfate ion PDB code: 5vu7(A).

Cluster 2 contains 2 ligand types

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Ligand		Description
		1. Ligand: EDO × 2 1,2-Ethanediol PDB codes: 6wyb(A),
		2. Ligand: TCE × 1 3,3',3''-Phosphanetriyltripropanoic acid PDB code: 6wyb(A).

Cluster 3 contains 1 ligand type

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Ligand		Description
		1. Ligand: TRS × 1 tromethamine 2-Amino-2-Hydroxymethyl-Propane-1,3-Diol PDB code: 6wya(A).

Cluster 4 contains 1 ligand type

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Ligand		Description
		1. Ligand: SO4 × 1 Sulfate ion PDB code: 6wyb(A).

Cluster 5 contains 1 ligand type

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Ligand		Description
		1. Ligand: EDO × 1 1,2-Ethanediol PDB code: 6wya(A).

Cluster 6 contains 1 ligand type

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Ligand		Description
		1. Ligand: EDO × 1 1,2-Ethanediol PDB code: 6wya(A).