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Ligand clusters for UniProt code P04050

Ligand clusters for P04050: DNA-directed RNA polymerase II subunit RPB1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RPO21 PE=1 SV=2

Top 6 (of 11) ligand clusters
Cluster 1.
15 ligand types
124 ligands
Cluster 2.
1 ligand type
3 ligands
Cluster 3.
1 ligand type
2 ligands
Cluster 4.
1 ligand type
2 ligands
Cluster 5.
1 ligand type
1 ligand
Cluster 6.
1 ligand type
1 ligand
Representative protein: 3gtgA  
 

Structures

PDB   Schematic diagram
3gtgA    
3gtjA    
2r7zA    
4a3gA    
3gtkA    
 more ...

 

 Cluster 1 contains 15 ligand types

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Ligand Description


 
1. Ligand: UTP × 4
Uridine 5'-Triphosphate
PDB codes: 1r9s(A), 1twf(A), 2nvz(A), 2yu9(A).


 
2. Ligand: GTP × 1
Guanosine-5'-Triphosphate
PDB code: 1twc(A).


 
3. Ligand: CTP × 1
Cytidine-5'-Triphosphate
PDB code: 1twg(A).


 
4. Ligand: ATP × 4
adenosine triphosphate
Adenosine-5'-Triphosphate
PDB codes: 1r9t(A), 1twa(A), 1twh(A), 3s1q(A).


 
5. Ligand: DUT × 1
Deoxyuridine-5'-Triphosphate
PDB code: 2nvx(A).


 
6. Ligand: G2P × 3
Phosphomethylphosphonic acid guanylate ester
PDB codes: 1y77(A), 2e2j(A), 2nvt(A).

_Mg
 
7. Metal: _MG × 82
PDB codes: 1i3q(A), 1i6h(A), 1r5u(A), 1r9s(A), 1r9t(A), 1sfo(A), 1wcm(A), 1y1w(A), 1y77(A), 2b63(A), 2e2h(A), 2e2i(A), 2e2j(A), 2ja5(A), 2ja6(A), 2ja7(A), 2ja8(A), 2nvq(A), 2nvt(A), 2nvx(A), 2nvz(A), 2r7z(A), 2r92(A), 2r93(A), 2vum(A), 2yu9(A), 3fki(A), 3gtg(A), 3gtj(A), 3gto(A), 3gtp(A), 3h3v(B), 3hov(A), 3how(A), 3hox(A), 3hoy(A), 3hoz(A), 3i4m(A), 3i4n(A), 3m3y(A), 3m4o(A), 3po2(A), 3po3(A), 3qt1(A), 3rzd(A), 3s14(A), 3s15(A), 3s16(A), 3s17(A), 3s1m(A), 3s1n(A), 3s1q(A), 3s1r(A), 3s2d(A), 3s2h(A), 4a3b(A), 4a3c(A), 4a3d(A), 4a3e(A), 4a3f(A), 4a3g(A), 4a3i(A), 4a3j(A), 4a3k(A), 4a3l(A), 4a3m(A), 4a93(A), 4bbr(A), 4bbs(A), 4bxx(A), 4by1(A), 4by7(A).

_Mn
 
8. Metal: _MN × 14
PDB codes: 1i50(A), 1k83(A), 1twa(A), 1twc(A), 1twf(A), 1twg(A), 1twh(A), 2nvy(A),


 
9. Ligand: APC × 5
Diphosphomethylphosphonic acid adenosyl ester
PDB codes: 4a3e(A), 4a3f(A), 4a3l(A), 4a3m(A), 4by1(A).


 
10. Ligand: G2P × 1
Phosphomethylphosphonic acid guanylate ester
PDB code: 4a3j(A).


 
11. Ligand: GTP × 2
Guanosine-5'-Triphosphate
PDB codes: 2e2h(A), 3s1r(A).


 
12. Ligand: C7P × 2
Cis-Diammine(pyridine)chloroplatinum(ii)
PDB codes: 3m3y(A), 3m4o(A).


 
13. Ligand: DUT × 1
Deoxyuridine-5'-Triphosphate
PDB code: 2nvq(A).


 
14. Ligand: __C-__A × 2
PDB codes: 4a3g(A), 4a3j(A).


 
15. Ligand: DGT × 1
2'-Deoxyguanosine-5'-Triphosphate
PDB code: 2e2i(A).

 

 Cluster 2 contains 1 ligand type

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Ligand Description


 
1. Ligand: ILX-TRX-GLY-ILE-GLY-CSX-ASN-HYP × 3
ILX=4,5-Dihydroxyisoleucine, TRX=6-Hydroxytryptophan, CSX=S-Oxy cysteine, HYP=4-Hydroxyproline.
PDB codes: 1k83(A), 2vum(A), 3cqz(A).

 

 Cluster 3 contains 1 ligand type

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Ligand Description


 
1. Ligand: EPE × 2
4-(2-Hydroxyethyl)-1-Piperazine ethanesulfonic acid
PDB codes: 3po3(A), 4by7(A).

 

 Cluster 4 contains 1 ligand type

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Ligand Description


 
1. Ligand: ACT × 2
acetic acid
Acetate ion
PDB codes: 3po2(A), 3po3(A).

 

 Cluster 5 contains 1 ligand type

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Ligand Description


 
1. Ligand: ACT × 1
acetic acid
Acetate ion
PDB code: 3po3(A).

 

 Cluster 6 contains 1 ligand type

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Ligand Description

_Zn
 
1. Metal: _ZN × 1
PDB code: 1i3q(A).

 

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