- Class: 3
- Architecture: 3.40:3-Layer(aba) Sandwich
- Topology: 3.40.470:Uracil-DNA Glycosylase, subunit E
- Homology: 3.40.470.10:Uracil-DNA glycosylase-like domain
PDB Entries
PDB ID | OPM | Mutant | Chain Formula | Resolution | HETNAM | |||
---|---|---|---|---|---|---|---|---|
Amino Acid sequence | SCOPe Family Level | CATH Homology Level | ||||||
1akz | [A] | [A] | [A] | 1.57 | ||||
1emh | [A](AB) | [A](AB) | [A](AB) | 1.8 | P2U:2___sq___-DEOXY-PSEUDOURIDINE-5___sq___MONOPHOSPHATE | |||
1emj | [A](AB) | [A](AB) | [A](AB) | 2 | ASU:4___sq___-THIO-2___sq___4___sq___-DIDEOXYRIBOFURANOSE-5___sq___-PHOSPHATE URA:URACIL | |||
1eug | [A] | [A] | [A] | 1.6 | ||||
1eui | [A2B2] | [A2B2] | [A2B2] | 3.2 | ||||
1flz | [A] | [A] | [A] | 2.3 | URA:URACIL | |||
1l9g | [A] | [A] | [A] | 2.5 | SF4:IRON/SULFUR CLUSTER SO4:SULFATE ION | |||
1lau | [A](A) | [A](A) | [A](A) | 1.8 | ||||
1lqg | [AB] | [AB] | [AB] | 2.9 | ||||
1lqj | [A] | [A] | [A] | 3.35 | ||||
1lqm | [AB] | [AB] | [AB] | 3.2 | ||||
1mtl | [A2](A2) | [A2](A2) | [A2](A2) | 2.8 | AAB:2___sq___-DEOXY-RIBOFURANOSE-5___sq___-MONOPHOSPHATE | |||
1mug | [A] | [A] | [A] | 1.8 | SO4:SULFATE ION | |||
1mwi | [A](A) | [A](A) | [A](A) | 2.35 | AAB:2___sq___-DEOXY-RIBOFURANOSE-5___sq___-MONOPHOSPHATE | |||
1mwj | [A](A) | [A](A) | [A](A) | 2.85 | ||||
1oe4 | [A2](AB) | [A2](AB) | [A2](AB) | 2 | 3DR:1___sq___,2___sq___-DIDEOXYRIBOFURANOSE-5___sq___-PHOSPHATE GOL:GLYCEROL IPA:ISOPROPYL ALCOHOL | |||
1oe5 | [A2](AB) | [A2](AB) | [A2](AB) | 2.3 | 3DR:1___sq___,2___sq___-DIDEOXYRIBOFURANOSE-5___sq___-PHOSPHATE DUR:2___sq___-DEOXYURIDINE EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID GOL:GLYCEROL IPA:ISOPROPYL ALCOHOL URA:URACIL | |||
1oe6 | [A2](AB) | [A2](AB) | [A2](AB) | 2.65 | 3DR:1___sq___,2___sq___-DIDEOXYRIBOFURANOSE-5___sq___-PHOSPHATE GOL:GLYCEROL HMU:5-HYDROXYMETHYL URACIL IPA:ISOPROPYL ALCOHOL | |||
1okb | [A] | [A] | [A] | 1.9 | CL:CHLORIDE ION GOL:GLYCEROL | |||
1q3f | [A](AB) | [A](AB) | [A](AB) | 1.9 | NRI:PHOSPHORIC ACID MONO-(4-HYDROXY-PYRROLIDIN-3-YLMETHYL)ESTER PO4:PHOSPHATE ION URA:URACIL | |||
1ssp | [A](AB) | [A](AB) | [A](AB) | 1.9 | ORP:2-DEOXY-5-PHOSPHONO-RIBOSE URA:URACIL | |||
1udg | [A] | [A] | [A] | 1.75 | SO4:SULFATE ION | |||
1udh | [A] | [A] | [A] | 1.75 | SO4:SULFATE ION URA:URACIL | |||
1udi | [AB] | [AB] | [AB] | 2.7 | ||||
1ugh | [AB] | [AB] | [AB] | 1.9 | ||||
1ui0 | [A] | [A] | [A] | 1.5 | SF4:IRON/SULFUR CLUSTER SO4:SULFATE ION URA:URACIL | |||
1ui1 | [A] | [A] | [A] | 2.8 | MSE:SELENOMETHIONINE SF4:IRON/SULFUR CLUSTER | |||
1uug | [AB] | [AB] | [AB] | 2.4 | ||||
1vk2 | [A] | [A] | [A] | 1.9 | MSE:SELENOMETHIONINE SF4:IRON/SULFUR CLUSTER UNL:UNKNOWN LIGAND | |||
1wyw | [AB] | [AB] | [AB] | 2.1 | CL:CHLORIDE ION MG:MAGNESIUM ION NA:SODIUM ION | |||
1yuo | [A] | [A] | [A] | 1.95 | ||||
2boo | [A] | [A] | [A] | 1.8 | NO3:NITRATE ION | |||
2c2p | [A] | [A] | [A] | 1.75 | ACT:ACETATE ION | |||
2c2q | [A] | [A] | [A] | 1.7 | ACT:ACETATE ION | |||
2c53 | [A] | [A] | [A] | 1.8 | DUR:2___sq___-DEOXYURIDINE GOL:GLYCEROL | |||
2c56 | [A] | [A] | [A] | 2.1 | FRU:BETA-D-FRUCTOFURANOSE GLC:ALPHA-D-GLUCOPYRANOSE | |||
2d07 | [AB] | [AB] | [AB] | 2.1 | ||||
2d3y | [A] | [A] | [A] | 1.55 | ACT:ACETATE ION DU:2___sq___-DEOXYURIDINE-5___sq___-MONOPHOSPHATE SF4:IRON/SULFUR CLUSTER | |||
2ddg | [A](AB) | [A](AB) | [A](AB) | 2.1 | 2HP:DIHYDROGENPHOSPHATE ION ACT:ACETATE ION EOH:ETHANOL GOL:GLYCEROL ORP:2-DEOXY-5-PHOSPHONO-RIBOSE SF4:IRON/SULFUR CLUSTER | |||
2dem | [A](AB) | [A](AB) | [A](AB) | 1.95 | 2HP:DIHYDROGENPHOSPHATE ION EOH:ETHANOL GOL:GLYCEROL ORP:2-DEOXY-5-PHOSPHONO-RIBOSE SF4:IRON/SULFUR CLUSTER | |||
2dp6 | [A](AB) | [A](AB) | [A](AB) | 1.8 | 2HP:DIHYDROGENPHOSPHATE ION EOH:ETHANOL GOL:GLYCEROL ORP:2-DEOXY-5-PHOSPHONO-RIBOSE SF4:IRON/SULFUR CLUSTER | |||
2eug | [A] | [A] | [A] | 1.5 | URA:URACIL | |||
2hxm | [A] | [A] | [A] | 1.3 | 302:4-[(1E,7E)-8-(2,6-DIOXO-1,2,3,6-TETRAHYDROPYRIMIDIN-4-YL)-3,6-DIOXA-2,7-DIAZAOCTA-1,7-DIEN-1-YL]BENZOIC ACID | |||
2j8x | [AB] | [AB] | [AB] | 2.3 | URE:UREA | |||
2jhq | [A] | [A] | [A] | 1.5 | CL:CHLORIDE ION | |||
2l3f | [A] | [A] | [A] | NOTAPPLICABLE. | ||||
2owq | [A2] | [A2] | [A2] | 2.4 | CL:CHLORIDE ION GOL:GLYCEROL IMD:IMIDAZOLE SO4:SULFATE ION | |||
2oxm | [A](AB) | [A](AB) | [A](AB) | 2.5 | 4MF:1-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-4-METHYL-1H-INDOLE | |||
2oyt | [A](AB) | [A](AB) | [A](AB) | 2 | 4MF:1-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-4-METHYL-1H-INDOLE AAB:2___sq___-DEOXY-RIBOFURANOSE-5___sq___-MONOPHOSPHATE | |||
2rba | [A2](AB) | [A2](AB) | [A2](AB) | 2.79 | 3DR:1___sq___,2___sq___-DIDEOXYRIBOFURANOSE-5___sq___-PHOSPHATE | |||
2ssp | [A](AB) | [A](AB) | [A](AB) | 2.25 | AAB:2___sq___-DEOXY-RIBOFURANOSE-5___sq___-MONOPHOSPHATE | |||
2uug | [AB] | [AB] | [AB] | 2.6 | ||||
2zhx | [AB] | [AB] | [AB] | 3.1 | ||||
3a7n | [A] | [A] | [A] | 1.95 | FLC:CITRATE ANION | |||
3cxm | [A] | [A] | [A] | 1.5 | BR:BROMIDE ION GOL:GLYCEROL URA:URACIL URB:5-BROMOPYRIMIDINE-2,4(1H,3H)-DIONE | |||
3eug | [A] | [A] | [A] | 1.43 | GOL:GLYCEROL | |||
3fcf | [A] | [A] | [A] | 1.84 | FCF:3-[(1E,7E)-8-(2,6-DIOXO-1,2,3,6-TETRAHYDROPYRIMIDIN-4-YL)-3,6-DIOXA-2,7-DIAZAOCTA-1,7-DIEN-1-YL]BENZOIC ACID SCN:THIOCYANATE ION | |||
3fci | [A] | [A] | [A] | 1.27 | 3FI:3-{(E)-[(3-{[(2,6-DIOXO-1,2,3,6-TETRAHYDROPYRIMIDIN-4-YL)METHYL]AMINO}PROPOXY)IMINO]METHYL}BENZOIC ACID NA:SODIUM ION SCN:THIOCYANATE ION | |||
3fck | [A] | [A] | [A] | 1.64 | FCK:3-({[3-({[(1E)-(2,6-DIOXO-1,2,3,6-TETRAHYDROPYRIMIDIN-4-YL)METHYLIDENE]AMINO}OXY)PROPYL]AMINO}METHYL)BENZOICACID | |||
3fcl | [A] | [A] | [A] | 1.7 | 3FL:3-{[(4-{[(2,6-DIOXO-1,2,3,6-TETRAHYDROPYRIMIDIN-4-YL)METHYL]AMINO}BUTYL)AMINO]METHYL}BENZOIC ACID SCN:THIOCYANATE ION | |||
3ikb | [A] | [A] | [A] | 1.67 | FLC:CITRATE ANION MSE:SELENOMETHIONINE | |||
3nt7 | [A2] | [A2] | [A2] | 2.4 | GOL:GLYCEROL SO4:SULFATE ION | |||
3tkb | [A] | [A] | [A] | 1.5 | IMD:IMIDAZOLE | |||
3tr7 | [A] | [A] | [A] | 2.2 | MSE:SELENOMETHIONINE | |||
3uf7 | [A][a2] | [A][a2] | [A][a2] | 1.2 | SO4:SULFATE ION | |||
3ufj | [A2](AB) | [A2](AB) | [A2](AB) | 2.97 | UF2:1-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)PYRIMIDINE-2,4(1H,3H)-DIONE | |||
3ufm | [A][a] | [A][a] | [A][a] | 1.95 | IOD:IODIDE ION | |||
3uo7 | [A2](AB) | [A2](AB) | [A2](AB) | 3 | 1CC:5-CARBOXY-2___sq___-DEOXYCYTIDINE MONOPHOSPHATE | |||
3uob | [A2](AB) | [A2](AB) | [A2](AB) | 3.01 | 1FC:4-AMINO-1-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)-2-OXO-1,2-DIHYDROPYRIMIDINE-5-CARBOXYLIC ACID | |||
3wdf | [A] | [A] | [A] | 1.48 | ||||
3wdg | [AB] | [AB] | [AB] | 2.2 | ||||
3zoq | [A2B] | [A2B] | [A2B] | 1.45 | CL:CHLORIDE ION GOL:GLYCEROL | |||
3zor | [A] | [A] | [A] | 2.95 | ||||
4dof | [A2] | [A2] | [A2] | 2.8 | ||||
4dog | [A2] | [A2] | [A2] | 2.3 | EDO:1,2-ETHANEDIOL SO4:SULFATE ION | |||
4eug | [A] | [A] | [A] | 1.4 | ||||
4fnc | [A](AB) | [A](AB) | [A](AB) | 2.49 | AAB:2___sq___-DEOXY-RIBOFURANOSE-5___sq___-MONOPHOSPHATE HMU:5-HYDROXYMETHYL URACIL | |||
4irb | [A2] | [A2] | [A2] | 2.3 | CL:CHLORIDE ION GOL:GLYCEROL SO4:SULFATE ION | |||
4jgc | [A](AB) | [A](AB) | [A](AB) | 2.58 | 1RT:4-AMINO-2-OXO-1,2-DIHYDROPYRIMIDINE-5-CARBOXYLIC ACID ORP:2-DEOXY-5-PHOSPHONO-RIBOSE | |||
4l5n | [A2B] | [A2B] | [A2B] | 2.16 | ACT:ACETATE ION | |||
4lyl | [AB] | [AB] | [AB] | 1.93 | ||||
4lzb | [A2] | [A2] | [A2] | 2.03 | CL:CHLORIDE ION DMS:DIMETHYL SULFOXIDE EDO:1,2-ETHANEDIOL K:POTASSIUM ION URA:URACIL | |||
4od8 | [AB] | [AB] | [AB] | 1.85 | GOL:GLYCEROL SO4:SULFATE ION | |||
4oda | [AB] | [AB] | [AB] | 2.2 | GOL:GLYCEROL SO4:SULFATE ION | |||
4qc9 | [A2] | [A2] | [A2] | 2.26 | EDO:1,2-ETHANEDIOL SO4:SULFATE ION | |||
4qca | [A2] | [A2] | [A2] | 1.9 | CL:CHLORIDE ION GOL:GLYCEROL K:POTASSIUM ION | |||
4qcb | [A](A2) | [A](A2) | [A](A2) | 2.89 | GOL:GLYCEROL | |||
4skn | [A](AB) | [A](AB) | [A](AB) | 2.9 | ORP:2-DEOXY-5-PHOSPHONO-RIBOSE URA:URACIL | |||
4uqm | [A](AB) | [A](AB) | [A](AB) | 1.35 | AAB:2___sq___-DEOXY-RIBOFURANOSE-5___sq___-MONOPHOSPHATE CL:CHLORIDE ION GOL:GLYCEROL | |||
4wpk | [A] | [A] | [A] | 0.98 | CIT:CITRIC ACID NA:SODIUM ION | |||
4wpl | [A] | [A] | [A] | 1.15 | ACT:ACETATE ION CL:CHLORIDE ION DMS:DIMETHYL SULFOXIDE GOL:GLYCEROL URA:URACIL | |||
4wru | [A] | [A] | [A] | 1.24 | CL:CHLORIDE ION GOL:GLYCEROL URA:URACIL | |||
4wrv | [A] | [A] | [A] | 1.44 | CL:CHLORIDE ION URA:URACIL | |||
4wrw | [A] | [A] | [A] | 1.9 | CL:CHLORIDE ION GOL:GLYCEROL | |||
4wrx | [A] | [A] | [A] | 1.4 | CL:CHLORIDE ION | |||
4wry | [A] | [A] | [A] | 1.43 | CIT:CITRIC ACID CL:CHLORIDE ION URF:5-FLUOROURACIL | |||
4wrz | [A] | [A] | [A] | 1.19 | CIT:CITRIC ACID CL:CHLORIDE ION IPA:ISOPROPYL ALCOHOL URF:5-FLUOROURACIL | |||
4ws0 | [A] | [A] | [A] | 1.97 | CL:CHLORIDE ION EDO:1,2-ETHANEDIOL URF:5-FLUOROURACIL | |||
4ws1 | [A] | [A] | [A] | 1.4 | CL:CHLORIDE ION EDO:1,2-ETHANEDIOL URF:5-FLUOROURACIL | |||
4ws2 | [A] | [A] | [A] | 1.13 | 6UA:6-AMINOPYRIMIDINE-2,4(3H,5H)-DIONE CIT:CITRIC ACID CL:CHLORIDE ION DMS:DIMETHYL SULFOXIDE IPA:ISOPROPYL ALCOHOL | |||
4ws3 | [A] | [A] | [A] | 1.4 | 6UA:6-AMINOPYRIMIDINE-2,4(3H,5H)-DIONE CL:CHLORIDE ION DMS:DIMETHYL SULFOXIDE | |||
4ws4 | [A] | [A] | [A] | 1.18 | 5NU:5-NITROURACIL CIT:CITRIC ACID CL:CHLORIDE ION DMS:DIMETHYL SULFOXIDE IPA:ISOPROPYL ALCOHOL | |||
4ws5 | [A] | [A] | [A] | 1.4 | 5NU:5-NITROURACIL CL:CHLORIDE ION | |||
4ws6 | [A] | [A] | [A] | 1.1 | CIT:CITRIC ACID CL:CHLORIDE ION DMS:DIMETHYL SULFOXIDE EDO:1,2-ETHANEDIOL IPA:ISOPROPYL ALCOHOL WBU:5-AMINO-1H-PYRIMIDINE-2,4-DIONE | |||
4ws7 | [A] | [A] | [A] | 1.88 | 5UC:5-CHLOROPYRIMIDINE-2,4(1H,3H)-DIONE CL:CHLORIDE ION EDO:1,2-ETHANEDIOL | |||
4ws8 | [A] | [A] | [A] | 1.4 | CL:CHLORIDE ION TUL:2-THIOXO-2,3-DIHYDROPYRIMIDIN-4(1H)-ONE | |||
4xeg | [A](AB) | [A](AB) | [A](AB) | 1.72 | ACY:ACETIC ACID EDO:1,2-ETHANEDIOL ORP:2-DEOXY-5-PHOSPHONO-RIBOSE | |||
4ygm | [AB] | [AB] | [AB] | 1.85 | SO4:SULFATE ION URA:URACIL | |||
4yig | [AB](AB) | [AB](AB) | [AB](AB) | 2.7 | ORP:2-DEOXY-5-PHOSPHONO-RIBOSE URA:URACIL | |||
4z3a | [A](AB) | [A](AB) | [A](AB) | 1.72 | AAB:2___sq___-DEOXY-RIBOFURANOSE-5___sq___-MONOPHOSPHATE ORP:2-DEOXY-5-PHOSPHONO-RIBOSE | |||
4z47 | [A](AB) | [A](AB) | [A](AB) | 1.45 | ACY:ACETIC ACID EDO:1,2-ETHANEDIOL ORP:2-DEOXY-5-PHOSPHONO-RIBOSE | |||
4z7b | [A](AB) | [A](AB) | [A](AB) | 2.02 | ACY:ACETIC ACID EDO:1,2-ETHANEDIOL ORP:2-DEOXY-5-PHOSPHONO-RIBOSE | |||
4z7z | [A](AB) | [A](AB) | [A](AB) | 1.83 | ACY:ACETIC ACID EDO:1,2-ETHANEDIOL ORP:2-DEOXY-5-PHOSPHONO-RIBOSE | |||
4zbx | [A] | [A] | [A] | 1.7 | MES:2-(N-MORPHOLINO)-ETHANESULFONIC ACID SF4:IRON/SULFUR CLUSTER | |||
4zby | [A] | [A] | [A] | 1.7 | MES:2-(N-MORPHOLINO)-ETHANESULFONIC ACID SF4:IRON/SULFUR CLUSTER URA:URACIL | |||
4zbz | [A] | [A] | [A] | 1.9 | GOL:GLYCEROL MES:2-(N-MORPHOLINO)-ETHANESULFONIC ACID SF4:IRON/SULFUR CLUSTER | |||
5ayr | [AB] | [AB] | [AB] | 2.4 | MG:MAGNESIUM ION | |||
5ays | [AB] | [AB] | [AB] | 2.09 | ||||
5cys | [A](AB) | [A](AB) | [A](AB) | 2.45 | ACY:ACETIC ACID ORP:2-DEOXY-5-PHOSPHONO-RIBOSE | |||
5eug | [A] | [A] | [A] | 1.6 | URA:URACIL | |||
5ff8 | [A](AB) | [A](AB) | [A](AB) | 1.7 | AAB:2___sq___-DEOXY-RIBOFURANOSE-5___sq___-MONOPHOSPHATE | |||
5h93 | [A] | [A] | [A] | 2.18 | ||||
5h98 | [A] | [A] | [A] | 2.04 | ||||
5h99 | [A] | [A] | [A] | 2.5 | ||||
5h9i | [A] | [A] | [A] | 1.5 | BME:BETA-MERCAPTOETHANOL GOL:GLYCEROL IPA:ISOPROPYL ALCOHOL LEA:PENTANOIC ACID XAN:XANTHINE | |||
5hf7 | [A](AB) | [A](AB) | [A](AB) | 1.54 | UF2:1-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)PYRIMIDINE-2,4(1H,3H)-DIONE | |||
5jk7 | [ABCD] | [ABCD] | [ABCD] | 3.49 | ||||
5jkr | [AB] | [AB] | [AB] | 2.6 | SO4:SULFATE ION | |||
5jks | [AB] | [AB] | [AB] | 2.79 | SO4:SULFATE ION | |||
5jkt | [AB] | [AB] | [AB] | 2.49 | ACT:ACETATE ION SO4:SULFATE ION | |||
5jx0 | [A2] | [A2] | [A2] | 2.4 | CL:CHLORIDE ION GOL:GLYCEROL | |||
5jx3 | [A2] | [A2] | [A2] | 2.3 | CL:CHLORIDE ION GOL:GLYCEROL | |||
5jx8 | [A2] | [A2] | [A2] | 2 | GOL:GLYCEROL SO4:SULFATE ION | |||
5jxy | [A](AB) | [A](AB) | [A](AB) | 1.71 | UF2:1-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)PYRIMIDINE-2,4(1H,3H)-DIONE | |||
5nn7 | [A] | [A] | [A] | 2.5 | ||||
5nnh | [A] | [A] | [A] | 2.2 | SO4:SULFATE ION | |||
5nnu | [A](AB) | [A](AB) | [A](AB) | 2.97 | AAB:2___sq___-DEOXY-RIBOFURANOSE-5___sq___-MONOPHOSPHATE | |||
5t2w | [A](AB) | [A](AB) | [A](AB) | 2.2 | XFC:4-AMINO-1-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)-2-OXO-1,2-DIHYDROPYRIMIDINE-5-CARBALDEHYDE |
*Chain Formula of OLIGAMI.
[ ] : Polypeptide - [AB] : Protein, [ab] : Small peptide
( ) : Nucleic acid - (AB) : DNA, (ab) : RNA
[ ] : Polypeptide - [AB] : Protein, [ab] : Small peptide
( ) : Nucleic acid - (AB) : DNA, (ab) : RNA