Ligand clusters for UniProt code Q9KEI9

Ligand clusters for Q9KEI9: Ribonuclease H from Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)

		Top 6 (of 15) ligand clusters Cluster 1. 15 ligand types 393 ligands Cluster 2. 10 ligand types 157 ligands Cluster 3. 5 ligand types 48 ligands Cluster 4. 4 ligand types 30 ligands Cluster 5. 4 ligand types 20 ligands Cluster 6. 2 ligand types 58 ligands
Representative protein: 2g8hA

Structures

PDB		Schematic diagram
2g8hA
6dmnA
6dmvA
6dozA
3uldA
		more ...

Cluster 1 contains 15 ligand types

Use checkboxes to select ligands to display in RasMol, Jmol, or download as an SDF file. Selection shortcuts: select all/none invert selection.
Ligand		Description
_Mg		1. Metal: _MG × 115 PDB codes: 1zbi(A), 2g8f(A), 2g8h(A), 2g8u(A), 2g8v(A), 2r7y(A), 3twh(A), 3uld(A), 4htu(A), 4hue(A), 4huf(A), 4hug(A), 5us2(A), 5usa(A), 5use(A), 5usg(A), 5w7n(A), 5w7o(A), 5wjr(A), 6dmv(A), 6do8(A), 6do9(A), 6doa(A), 6dob(A), 6doc(A), 6dod(A), 6doe(A), 6dof(A), 6dog(A), 6doj(A), 6dok(A), 6dol(A), 6dom(A), 6don(A), 6doo(A), 6dop(A), 6doq(A), 6dor(A), 6dos(A), 6dot(A), 6dou(A), 6dov(A), 6dow(A), 6dox(A), 6doz(A), 6dp0(A), 6dp1(A), 6dp2(A), 6dp3(A), 6dp4(A), 6dp5(A), 6dp6(A), 6dp8(A), 6dph(A), 6dpi(A), 6dpl(A), 6dpm(A), 6dpn(A), 6dpo(A), 6dpp(A),
__K		2. Metal: __K × 65 PDB codes: 6dmv(A), 6do8(A), 6do9(A), 6doa(A), 6dob(A), 6doc(A), 6dod(A), 6doe(A), 6dof(A), 6dog(A), 6doh(A), 6doi(A), 6doj(A), 6dok(A), 6dol(A), 6dom(A), 6don(A), 6doo(A), 6dop(A), 6doq(A), 6dor(A), 6dos(A), 6doz(A), 6dp0(A), 6dp1(A), 6dp2(A), 6dp3(A), 6dp4(A), 6dp5(A), 6dp6(A), 6dp7(A), 6dp9(A), 6dpa(A), 6dpb(A), 6dpc(A), 6dpd(A), 6dpe(A), 6dpf(A), 6dph(A), 6dpj(A), 6dpk(A), 6dpn(A).
		3. Ligand: GOL × 63 glycerin Glycerol PDB codes: 4htu(A), 4hue(A), 4huf(A), 4hug(A), 4opj(A), 5vaj(A), 6dmv(A), 6do8(A), 6do9(A), 6doa(A), 6dob(A), 6doc(A), 6dod(A), 6doe(A), 6dof(A), 6dog(A), 6doh(A), 6doi(A), 6doj(A), 6dok(A), 6dol(A), 6dom(A), 6don(A), 6doo(A), 6dop(A), 6doq(A), 6dor(A), 6dos(A), 6dot(A), 6dou(A), 6dov(A), 6dow(A), 6dox(A), 6doy(A), 6doz(A), 6dp0(A), 6dp1(A), 6dp2(A), 6dp3(A), 6dp4(A), 6dp5(A), 6dp8(A), 6dp9(A), 6dpa(A), 6dpb(A), 6dpc(A), 6dpd(A), 6dpe(A), 6dpf(A), 6dpg(A), 6dph(A), 6dpi(A), 6dpj(A), 6dpk(A), 6dpl(A), 6dpm(A), 6dpn(A), 6dpo(A), 6dpp(A).
_Mn		4. Metal: _MN × 29 PDB codes: 2g8i(A), 6dp7(A), 6dp9(A), 6dpa(A), 6dpb(A), 6dpc(A), 6dpd(A), 6dpe(A), 6dpf(A), 6dpg(A), 6dpj(A), 6dpk(A),
		5. Ligand: __C-__G × 53 PDB codes: 6dmv(A), 6do8(A), 6do9(A), 6doa(A), 6dob(A), 6doc(A), 6dod(A), 6doe(A), 6dof(A), 6dog(A), 6doh(A), 6doi(A), 6doj(A), 6dok(A), 6dol(A), 6dom(A), 6don(A), 6doo(A), 6dop(A), 6doq(A), 6dor(A), 6dos(A), 6dot(A), 6dou(A), 6dov(A), 6dow(A), 6dox(A), 6doz(A), 6dp0(A), 6dp1(A), 6dp2(A), 6dp3(A), 6dp4(A), 6dp5(A), 6dp6(A), 6dp8(A), 6dp9(A), 6dpa(A), 6dpb(A), 6dpc(A), 6dpd(A), 6dpe(A), 6dpf(A), 6dpg(A), 6dph(A), 6dpi(A), 6dpj(A), 6dpk(A), 6dpl(A), 6dpm(A), 6dpn(A), 6dpo(A), 6dpp(A).
_Rb		6. Metal: _RB × 19 PDB codes: 6dot(A), 6dou(A), 6dov(A), 6dow(A), 6dox(A), 6dpi(A), 6dpl(A), 6dpm(A), 6dpp(A),
		7. Ligand: EDO × 17 1,2-Ethanediol PDB codes: 6dmn(A), 6doa(A), 6dob(A), 6doc(A), 6dod(A), 6doe(A), 6dof(A), 6dog(A), 6dom(A), 6don(A), 6doy(A), 6dp7(A), 6dpj(A), 6dpl(A),
		8. Ligand: PGE × 14 Triethylene glycol PDB codes: 6do9(A), 6doa(A), 6dob(A), 6doc(A), 6dod(A), 6doe(A), 6dof(A), 6dog(A), 6doo(A), 6dop(A), 6doq(A), 6dor(A), 6dos(A), 6dph(A).
_Ca		9. Metal: _CA × 8 PDB codes: 2g8k(A), 2g8w(A), 6dmn(A), 6doh(A), 6doi(A).
_Li		10. Metal: _LI × 3 PDB codes: 6doy(A), 6dp8(A).
		11. Ligand: __C × 2 PDB codes: 6dmn(A), 6dp7(A).
		12. Ligand: __G × 2 PDB codes: 6dmn(A), 6dp7(A).
		13. Ligand: ACT × 1 Acetate ion PDB code: 5vaj(A).
		14. Ligand: GF2-AF2-CFZ-AF2-CFZ-CFZ-UFT-GF2-AF2-UFT-UFT-CFZ × 1 GF2=2'-Deoxy-2'-Fluoroguanosine 5'-(Dihydrogen phosphate), AF2=2'-Deoxy-2'-Fluoroadenosine 5'-(Dihydrogen phosphate), CFZ=2'-Deoxy-2'-Fluorocytidine 5'-(Dihydrogen phosphate), UFT=2'-Deoxy-2'-Fluorouridine 5'-(Dihydrogen phosphate). PDB code: 5swm(A).
_Na		15. Metal: _NA × 1 PDB code: 5swm(A).

Cluster 2 contains 10 ligand types

Selection shortcuts: select all/none invert selection.
Ligand		Description
		1. Ligand: GOL × 90 glycerin Glycerol PDB codes: 3i8d(A), 5vaj(A), 6dmv(A), 6do8(A), 6do9(A), 6doa(A), 6dob(A), 6doc(A), 6dod(A), 6doe(A), 6dof(A), 6dog(A), 6doh(A), 6doi(A), 6doj(A), 6dok(A), 6dol(A), 6dom(A), 6don(A), 6doo(A), 6dop(A), 6doq(A), 6dor(A), 6dos(A), 6dot(A), 6dou(A), 6dov(A), 6dow(A), 6dox(A), 6doz(A), 6dp0(A), 6dp1(A), 6dp2(A), 6dp3(A), 6dp4(A), 6dp8(A), 6dp9(A), 6dpa(A), 6dpb(A), 6dpc(A), 6dpd(A), 6dpe(A), 6dpf(A), 6dph(A), 6dpi(A), 6dpk(A), 6dpl(A), 6dpm(A), 6dpn(A), 6dpo(A), 6dpp(A),
_Mg		2. Metal: _MG × 1 PDB code: 3uld(A).
Iod		3. Metal: IOD × 29 PDB codes: 6dmv(A), 6do8(A), 6do9(A), 6doa(A), 6dob(A), 6doc(A), 6dod(A), 6dog(A), 6doh(A), 6doi(A), 6dok(A), 6dol(A), 6dom(A), 6don(A), 6doo(A), 6doz(A), 6dp0(A), 6dp1(A), 6dp2(A), 6dp4(A), 6dp5(A), 6dp6(A), 6dp7(A), 6dpa(A), 6dpg(A), 6dph(A), 6dpk(A), 6dpn(A), 6dpo(A).
		4. Ligand: EDO × 13 1,2-Ethanediol PDB codes: 6dmn(A), 6doh(A), 6doy(A), 6dp3(A), 6dp5(A), 6dp6(A), 6dp8(A), 6dph(A), 6dpl(A), 6dpm(A), 6dpp(A).
_Cl		5. Metal: _CL × 12 PDB codes: 2g8f(A), 2g8i(A), 6dot(A), 6dou(A), 6dov(A), 6dow(A), 6dox(A), 6dp8(A), 6dpi(A), 6dpl(A), 6dpm(A), 6dpp(A).
_Rb		6. Metal: _RB × 8 PDB codes: 6dot(A), 6dou(A), 6dov(A), 6dow(A), 6dox(A), 6dpi(A), 6dpm(A), 6dpp(A).
		7. Ligand: MPD × 1 (4s)-2-Methyl-2,4-Pentanediol PDB code: 2g8i(A).
		8. Ligand: PEG × 1 Di(hydroxyethyl)ether PDB code: 5swm(A).
		9. Ligand: VO4-VO4-VO4-VO4-VO4-VO4 × 1 VO4=Vanadate ion. PDB code: 2g8h(A).
_Ca		10. Metal: _CA × 1 PDB code: 2g8k(A).

Cluster 3 contains 5 ligand types

Selection shortcuts: select all/none invert selection.
Ligand		Description
		1. Ligand: GOL × 10 glycerin Glycerol PDB codes: 6dmn(A), 6dmv(A), 6do8(A), 6dok(A), 6dol(A), 6dot(A), 6dp1(A), 6dp4(A), 6dpn(A), 6dpo(A).
		2. Ligand: EDO × 34 1,2-Ethanediol PDB codes: 6do9(A), 6doa(A), 6dob(A), 6doc(A), 6dod(A), 6doe(A), 6dof(A), 6dog(A), 6doh(A), 6doi(A), 6dom(A), 6don(A), 6doo(A), 6dop(A), 6doq(A), 6dor(A), 6dos(A), 6dou(A), 6dow(A), 6dox(A), 6doy(A), 6dp8(A), 6dpb(A), 6dpc(A), 6dpd(A), 6dpe(A), 6dpf(A), 6dpg(A), 6dph(A), 6dpi(A), 6dpk(A), 6dpl(A), 6dpm(A), 6dpp(A).
		3. Ligand: PO4 × 2 Phosphate ion PDB codes: 2r7y(A), 3twh(A).
		4. Ligand: EDO-GOL × 1 GOL=Glycerol, EDO=1,2-Ethanediol. PDB code: 6dp3(A).
		5. Ligand: SO4 × 1 Sulfate ion PDB code: 1zbf(A).

Cluster 4 contains 4 ligand types

Selection shortcuts: select all/none invert selection.
Ligand		Description
		1. Ligand: GOL × 18 glycerin Glycerol PDB codes: 6do9(A), 6doa(A), 6dob(A), 6doc(A), 6dod(A), 6doe(A), 6dof(A), 6dog(A), 6dom(A), 6don(A), 6doo(A), 6dop(A), 6doq(A), 6dor(A), 6dos(A), 6dp4(A), 6dp5(A), 6dpl(A).
		2. Ligand: EDO × 7 1,2-Ethanediol PDB codes: 6doh(A), 6doi(A), 6doj(A), 6dp3(A), 6dpa(A), 6dph(A), 6dpk(A).
		3. Ligand: PGE × 3 Triethylene glycol PDB codes: 6dpd(A), 6dpe(A), 6dpf(A).
		4. Ligand: PEG × 2 Di(hydroxyethyl)ether PDB codes: 6dox(A), 6dp8(A).

Cluster 5 contains 4 ligand types

Selection shortcuts: select all/none invert selection.
Ligand		Description
_Mn		1. Metal: _MN × 9 PDB codes: 2g8i(A), 6dp7(A), 6dpb(A), 6dpc(A), 6dpd(A), 6dpe(A), 6dpf(A), 6dpg(A), 6dpk(A).
		2. Ligand: GOL × 2 glycerin Glycerol PDB codes: 6dp3(A),
		3. Ligand: EDO × 8 1,2-Ethanediol PDB codes: 6dp3(A), 6dp8(A), 6dpd(A), 6dpf(A), 6dpg(A), 6dpk(A), 6dpo(A).
		4. Ligand: PEG × 1 Di(hydroxyethyl)ether PDB code: 6dp8(A).

Cluster 6 contains 2 ligand types

Selection shortcuts: select all/none invert selection.
Ligand		Description
		1. Ligand: GOL × 16 glycerin Glycerol PDB codes: 4hue(A), 5vaj(A), 6do9(A), 6doh(A), 6doi(A), 6dom(A), 6don(A), 6doo(A), 6dop(A), 6doq(A), 6dor(A), 6dos(A), 6dp3(A), 6dp4(A), 6dph(A).
		2. Ligand: EDO × 42 1,2-Ethanediol PDB codes: 6dmn(A), 6dmv(A), 6do8(A), 6doa(A), 6dob(A), 6doc(A), 6dod(A), 6doe(A), 6dof(A), 6dog(A), 6doj(A), 6dok(A), 6dol(A), 6dot(A), 6dou(A), 6dov(A), 6dow(A), 6dox(A), 6doy(A), 6doz(A), 6dp0(A), 6dp1(A), 6dp2(A), 6dp5(A), 6dp8(A), 6dp9(A), 6dpa(A), 6dpb(A), 6dpc(A), 6dpd(A), 6dpe(A), 6dpf(A), 6dpg(A), 6dpi(A), 6dpj(A), 6dpk(A), 6dpl(A), 6dpm(A), 6dpn(A), 6dpo(A), 6dpp(A).