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EBI Databases Structure Databases PDBsum

Ligand clusters for UniProt code Q97W02

Ligand clusters for Q97W02: DNA polymerase IV from Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)

Top 6 (of 26) ligand clusters
Cluster 1.
39 ligand types
363 ligands
 Cluster 2.
2 ligand types
2 ligands
 Cluster 3.
1 ligand type
1 ligand
 Cluster 4.
2 ligand types
2 ligands
 Cluster 5.
2 ligand types
2 ligands
 Cluster 6.
4 ligand types
101 ligands
Representative protein: 3fdsA  
JSmol
 

Structures

PDB   Schematic diagram
3fdsA    
2rdiA    
2j6uA    
3pw7A    
2jeiA    
 more ...

 

 Cluster 1 contains 39 ligand types (of which only 20 are listed. Click for all)

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Ligand Description


 
1. Ligand: DGT × 12
2'-Deoxyguanosine-5'-Triphosphate
PDB codes: 2agp(A), 2c22(A), 2j6u(A), 2jef(A), 2jeg(A), 2jei(A), 2jej(A), 2uvr(A), 2uvu(A), 2uvv(A), 2uvw(A), 2va3(A).


 
2. Ligand: DCP × 5
2'-Deoxycytidine-5'-Triphosphate
PDB codes: 1s0n(A), 1s10(A), 2asd(A), 2atl(A), 2c2e(A).


 
3. Ligand: DTP × 7
2'-Deoxyadenosine 5'-Triphosphate
PDB codes: 1s0m(A), 2agq(A), 2bqr(A), 2c2d(A), 2j6s(A), 2j6t(A).


 
4. Ligand: TTP × 1
Thymidine-5'-Triphosphate
PDB code: 1s0o(A).


 
5. Ligand: POP × 2
Pyrophosphate 2-
PDB codes: 2ago(A), 2ibk(A).

_Mg
 
6. Metal: _MG × 29
PDB codes: 1jxl(A), 1n56(A), 1s0m(A), 2ago(A), 2agp(A), 2agq(A), 2w8k(A), 2w8l(A), 2w9a(A), 2w9b(A), 2w9c(A), 2xca(A), 2xcp(A), 3v6h(A), 3v6j(A), 3v6k(A), 4tqr(A), 4tqs(A),


 
7. Ligand: GOL × 6
glycerin
Glycerol
PDB codes: 2ibk(A), 2rdi(A), 2rdj(A), 3fds(A), 3m9m(B), 4qwb(A).


 
8. Ligand: TRS × 1
tromethamine
2-Amino-2-Hydroxymethyl-Propane-1,3-Diol
PDB code: 4rzr(A).


 
9. Ligand: ATP × 5
Adenosine-5'-Triphosphate
PDB codes: 1n48(A), 1n56(A), 1ryr(A), 1rys(A), 2ia6(A).


 
10. Ligand: DAD × 1
2',3'-Dideoxyadenosine-5'-Triphosphate
PDB code: 2bqu(A).


 
11. Ligand: DG3 × 1
2'-3'-Dideoxyguanosine-5'-Triphosphate
PDB code: 1jxl(A).


 
12. Ligand: DCT × 4
2',3'-Dideoxycytidine 5'-Triphosphate
PDB codes: 1s97(A), 2c2r(A), 2v9w(A), 2va2(A).


 
13. Ligand: ADI × 1
2',3'-Dideoxyadenosine-5'-Diphosphate
PDB code: 1jx4(A).


 
14. Ligand: DDY × 1
2',3'-Dideoxycytosine-5'-Diphosphate
PDB code: 1s9f(A).


 
15. Ligand: BAP × 1
1,2,3-Trihydroxy-1,2,3,4-Tetrahydrobenzo[a]pyrene
PDB code: 2ibk(A).


 
16. Ligand: EDO × 5
1,2-Ethanediol
PDB codes: 2ibk(A), 2imw(P),

_Ca
 
17. Metal: _CA × 193
PDB codes: 1jx4(A), 1jxl(A), 1n48(A), 1ryr(A), 1rys(A), 1s0m(A), 1s0n(A), 1s0o(A), 1s10(A), 1s97(A), 1s9f(A), 2ago(A), 2agp(A), 2agq(A), 2asd(A), 2asj(A), 2asl(A), 2atl(A), 2au0(A), 2bq3(A), 2bqr(A), 2bqu(A), 2c22(A), 2c2d(A), 2c2e(A), 2c2r(A), 2ia6(A), 2ibk(A), 2imw(P), 2j6s(A), 2j6t(A), 2j6u(A), 2jef(A), 2jeg(A), 2jei(A), 2jej(A), 2r8g(A), 2r8h(A), 2r8i(A), 2rdj(A), 2uvr(A), 2uvu(A), 2uvv(A), 2uvw(A), 2v4q(A), 2v4r(A), 2v9w(A), 2va2(A), 2va3(A), 3gii(A), 3gij(A), 3gik(A), 3gil(A), 3gim(A), 3khg(A), 3khh(A), 3khl(A), 3khr(A), 3m9m(B), 3m9n(B), 3m9o(B), 3pr4(A), 3pr5(B), 3pvx(A), 3pw0(A), 3pw2(A), 3pw4(A), 3pw5(A), 3pw7(A), 3qz7(A), 3qz8(A), 3raq(A), 3rax(A), 3rb0(A), 3rb3(A), 3rb4(A), 3rb6(A), 3rbd(A), 3rbe(A), 3t5h(A), 3t5j(A), 3t5k(A), 3t5l(A), 4f4w(A), 4f4x(A), 4f4y(A), 4f4z(B), 4f50(A), 4fbt(A), 4fbu(A), 4g3i(A), 4gc6(A), 4gc7(A), 4juz(A), 4jv0(A), 4jv1(A), 4jv2(A), 4qw8(A), 4qw9(A), 4qwa(A), 4qwb(A), 4qwc(A), 4qwd(A), 4qwe(A), 4rua(A), 4ruc(A), 4rzr(A), 5edw(A), 6l84(A),


 
18. Ligand: DGT × 28
2'-Deoxyguanosine-5'-Triphosphate
PDB codes: 2r8g(A), 2r8h(A), 2v4q(A), 2v4r(A), 2w8k(A), 2w8l(A), 2w9a(A), 2xca(A), 3gii(A), 3gij(A), 3gik(A), 3gil(A), 3gim(A), 3khg(A), 3khh(A), 3raq(A), 3rax(A), 3rb0(A), 3rb3(A), 3rb4(A), 3rb6(A), 3rbd(A), 3rbe(A), 3t5h(A), 3t5l(A), 4fbt(A), 4juz(A), 4jv1(A).


 
19. Ligand: DCP × 11
2'-Deoxycytidine-5'-Triphosphate
PDB codes: 2xcp(A), 3pw7(A), 3qz7(A), 3qz8(A), 3v6h(A), 3v6j(A), 4f4w(A), 4f4x(A), 4f4y(A), 4qw8(A), 4tqs(A).


 
20. Ligand: DTP × 9
2'-Deoxyadenosine 5'-Triphosphate
PDB codes: 2r8i(A), 3pw0(A), 3pw4(A), 3t5j(A), 3t5k(A), 4jv0(A), 4jv2(A), 4rua(A), 4ruc(A).

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 Cluster 2 contains 2 ligand types

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Ligand Description


 
1. Ligand: 0DG-0DG-0DA-0DA-0DT-0DC-0DC-0DT-0DT-0DC-0DC-0DC-0DC-0DC × 1
0DG=2'-Deoxy-L-Ribo-Furanosyl guanine-5'-Monophosphate, 0DA=2'-Deoxy-L-Ribo-Furanosyl adenosine-5'-Monophosphate, 0DT=2'-Deoxy-L-Ribo-Furanosyl thymidine-5'-Monophosphate, 0DC=2'-Deoxy-L-Ribo-Furanosyl cytosine-5'-Monophosphate.
PDB code: 6l97(A).


 
2. Ligand: 0DG-0DG-0DG-0DG-0DG-0DA-0DA-0DG-0DG-0DA-0DT-0DT-0DC-0DC × 1
0DG=2'-Deoxy-L-Ribo-Furanosyl guanine-5'-Monophosphate, 0DA=2'-Deoxy-L-Ribo-Furanosyl adenosine-5'-Monophosphate, 0DT=2'-Deoxy-L-Ribo-Furanosyl thymidine-5'-Monophosphate, 0DC=2'-Deoxy-L-Ribo-Furanosyl cytosine-5'-Monophosphate.
PDB code: 6l97(A).

 

 Cluster 3 contains 1 ligand type

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Ligand Description


 
1. Ligand: 1PE × 1
Pentaethylene glycol
PDB code: 3fds(A).

 

 Cluster 4 contains 2 ligand types

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Ligand Description


 
1. Ligand: GOL × 1
glycerin
Glycerol
PDB code: 3fds(A).


 
2. Ligand: EDO × 1
1,2-Ethanediol
PDB code: 2ibk(A).

 

 Cluster 5 contains 2 ligand types

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Ligand Description


 
1. Ligand: PO4 × 1
Phosphate ion
PDB code: 2ia6(A).


 
2. Ligand: EDO × 1
1,2-Ethanediol
PDB code: 3fds(A).

 

 Cluster 6 contains 4 ligand types

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Ligand Description

_Mg
 
1. Metal: _MG × 12
PDB codes: 1jx4(A), 1jxl(A), 1s9f(A), 2ago(A), 2agp(A), 2w8k(A), 2w8l(A), 2w9a(A), 2w9b(A), 2w9c(A), 2xca(A), 4tqr(A).

_Ca
 
2. Metal: _CA × 87
PDB codes: 1s0m(A), 1s0n(A), 1s0o(A), 2agq(A), 2asd(A), 2atl(A), 2bq3(A), 2bqr(A), 2bqu(A), 2c22(A), 2c2d(A), 2c2e(A), 2c2r(A), 2ia6(A), 2imw(P), 2j6s(A), 2j6t(A), 2j6u(A), 2jef(A), 2jeg(A), 2jei(A), 2jej(A), 2r8g(A), 2r8h(A), 2r8i(A), 2rdj(A), 2uvr(A), 2uvu(A), 2uvv(A), 2uvw(A), 2v4q(A), 2v4r(A), 2va2(A), 2va3(A), 3gii(A), 3gij(A), 3gik(A), 3gil(A), 3gim(A), 3khg(A), 3khh(A), 3khl(A), 3khr(A), 3m9m(B), 3m9n(B), 3m9o(B), 3pr4(A), 3pr5(B), 3pvx(A), 3pw0(A), 3pw2(A), 3pw4(A), 3pw5(A), 3qz7(A), 3qz8(A), 3raq(A), 3rax(A), 3rb0(A), 3rb3(A), 3rb4(A), 3rb6(A), 3rbd(A), 3rbe(A), 3t5h(A), 3t5j(A), 3t5k(A), 3t5l(A), 3v6h(A), 3v6k(A), 4f4z(B), 4fbt(A), 4gc6(A), 4gc7(A), 4juz(A), 4jv0(A), 4jv1(A), 4jv2(A), 4qw8(A), 4qw9(A), 4qwa(A), 4qwb(A), 4qwd(A), 4qwe(A), 4rua(A), 4ruc(A), 5edw(A), 6l84(A).


 
3. Ligand: ACT × 1
Acetate ion
PDB code: 4qwc(A).

_Na
 
4. Metal: _NA × 1
PDB code: 4rzr(A).

 

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