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Ligand clusters for UniProt code P08518

Ligand clusters for P08518: DNA-directed RNA polymerase II subunit RPB2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RPB2 PE=1 SV=2

6 ligand clusters
Cluster 1.
15 ligand types
38 ligands
Cluster 2.
1 ligand type
3 ligands
Cluster 3.
1 ligand type
1 ligand
Cluster 4.
1 ligand type
1 ligand
Cluster 5.
1 ligand type
10 ligands
Cluster 6.
1 ligand type
83 ligands
Representative protein: 3gtgB  
 

Structures

PDB   Schematic diagram
3gtgB    
4by1B    
3gtjB    
3i4mB    
3s1mB    
 more ...

 

 Cluster 1 contains 15 ligand types

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Ligand Description


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


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


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


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


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


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


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

_Mg
 
8. Metal: _MG × 5
PDB codes: 1r9t(B), 2e2h(B), 2nvz(B), 3s15(B), 3s1q(B).

_Mn
 
9. Metal: _MN × 5
PDB codes: 1twa(B), 1twc(B), 1twf(B), 1twg(B), 1twh(B).


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


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


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


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


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


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

 

 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(B), 2vum(B), 3cqz(B).

 

 Cluster 3 contains 1 ligand type

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Ligand Description


 
1. Ligand: EPE × 1
4-(2-Hydroxyethyl)-1-Piperazine ethanesulfonic acid
PDB code: 3po3(B).

 

 Cluster 4 contains 1 ligand type

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Ligand Description


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

 

 Cluster 5 contains 1 ligand type

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Ligand Description

_Zn
 
1. Metal: _ZN × 10
PDB codes: 1i3q(B), 1i50(B), 1k83(B), 1twa(B), 1twc(B), 1twf(B), 1twg(B), 1twh(B), 2nvy(B), 3cqz(B).

 

 Cluster 6 contains 1 ligand type

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Ligand Description

_Zn
 
1. Metal: _ZN × 83
PDB codes: 1i6h(B), 1nik(B), 1r5u(B), 1r9s(B), 1r9t(B), 1sfo(B), 1wcm(B), 1y1v(B), 1y1w(B), 1y77(B), 2b63(B), 2b8k(B), 2e2h(B), 2e2i(B), 2e2j(B), 2ja5(B), 2ja6(B), 2ja7(B), 2ja8(B), 2nvq(B), 2nvt(B), 2nvz(B), 2r7z(B), 2r92(B), 2r93(B), 2vum(B), 2yu9(B), 3fki(B), 3gtg(B), 3gtj(B), 3gtk(B), 3gtl(B), 3gtm(B), 3gto(B), 3gtp(B), 3gtq(B), 3h3v(C), 3hou(B), 3hov(B), 3how(B), 3hox(B), 3hoy(B), 3hoz(B), 3i4m(B), 3i4n(B), 3j0k(B), 3k1f(B), 3k7a(B), 3m3y(B), 3m4o(B), 3po2(B), 3po3(B), 3qt1(B), 3rzd(B), 3rzo(B), 3s14(B), 3s15(B), 3s16(B), 3s17(B), 3s1m(B), 3s1n(B), 3s1q(B), 3s1r(B), 3s2d(B), 3s2h(B), 4a3b(B), 4a3c(B), 4a3d(B), 4a3e(B), 4a3f(B), 4a3g(B), 4a3i(B), 4a3j(B), 4a3k(B), 4a3l(B), 4a3m(B), 4a93(B), 4bbr(B), 4bbs(B), 4bxx(B), 4bxz(B), 4by1(B), 4by7(B).

 

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