- Class: 3
- Architecture: 3.40:3-Layer(aba) Sandwich
- Topology: 3.40.1030:Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2
- Homology: 3.40.1030.10:Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain
PDB Entries
| PDB ID | OPM | Mutant | Chain Formula | Resolution | HETNAM | |||
|---|---|---|---|---|---|---|---|---|
| Amino Acid sequence | SCOPe Family Level | CATH Homology Level | ||||||
| 1azy | [A2] | [A2] | [A2] | 3 | ||||
| 1brw | [A2] | [A2] | [A2] | 2.1 | CA:CALCIUM ION MES:2-(N-MORPHOLINO)-ETHANESULFONIC ACID PO4:PHOSPHATE ION URA:URACIL | |||
| 1gxb | [A2] | [A2] | [A2] | 2.65 | MG:MAGNESIUM ION POP:PYROPHOSPHATE 2- | |||
| 1kgz | [A2] | [A2] | [A2] | 2.4 | HG:MERCURY (II) ION MN:MANGANESE (II) ION PRP:1-O-PYROPHOSPHONO-5-O-PHOSPHONO-ALPHA-D-RIBOFURANOSE | |||
| 1khd | [A2] | [A2] | [A2] | 1.86 | ||||
| 1o17 | [A2] | [A2] | [A2] | 2.05 | ||||
| 1otp | [A2] | [A2] | [A2] | 2.8 | ||||
| 1uou | [A2] | [A2] | [A2] | 2.11 | CMU:5-CHLORO-6-(1-(2-IMINOPYRROLIDINYL) METHYL)URACIL | |||
| 1v8g | [A2] | [A2] | [A2] | 2.1 | ||||
| 1vqu | [A2] | [A2] | [A2] | 1.85 | ACT:ACETATE ION GOL:GLYCEROL MSE:SELENOMETHIONINE | |||
| 1zvw | [A] | [A] | [A] | 2.3 | BEN:BENZAMIDINE MG:MAGNESIUM ION MSE:SELENOMETHIONINE PRP:1-O-PYROPHOSPHONO-5-O-PHOSPHONO-ALPHA-D-RIBOFURANOSE | |||
| 1zxy | [A2] | [A2] | [A2] | 2.56 | MG:MAGNESIUM ION PRP:1-O-PYROPHOSPHONO-5-O-PHOSPHONO-ALPHA-D-RIBOFURANOSE | |||
| 1zyk | [A2] | [A2] | [A2] | 2.4 | BE2:2-AMINOBENZOIC ACID MG:MAGNESIUM ION PRP:1-O-PYROPHOSPHONO-5-O-PHOSPHONO-ALPHA-D-RIBOFURANOSE | |||
| 2bpq | [A2] | [A2] | [A2] | 1.9 | BEN:BENZAMIDINE GOL:GLYCEROL | |||
| 2dsj | [A2] | [A2] | [A2] | 1.8 | CL:CHLORIDE ION | |||
| 2elc | [A4] | [A4] | [A4] | 1.55 | GOL:GLYCEROL NA:SODIUM ION | |||
| 2gvq | [A2] | [A2] | [A2] | 2.43 | BE2:2-AMINOBENZOIC ACID | |||
| 2j0f | [A2] | [A2] | [A2] | 2.31 | TDR:THYMINE | |||
| 2tpt | [A2] | [A2] | [A2] | 2.6 | SO4:SULFATE ION | |||
| 2wk5 | [A] | [A] | [A] | 2.99 | GOL:GLYCEROL | |||
| 2wk6 | [A2] | [A2] | [A2] | 2.5 | IUR:5-IODOURACIL | |||
| 3gbr |  | [A2] | [A2] | [A2] | 2.25 | GOL:GLYCEROL MN:MANGANESE (II) ION PEG:DI(HYDROXYETHYL)ETHER PRP:1-O-PYROPHOSPHONO-5-O-PHOSPHONO-ALPHA-D-RIBOFURANOSE | ||
| 3h5q | | [A2] | [A2] | [A2] | 1.94 | MSE:SELENOMETHIONINE SO4:SULFATE ION THM:THYMIDINE | ||
| 3qqs | [A2] | [A2] | [A2] | 1.97 | 17C:2,2___sq___-IMINODIBENZOIC ACID DPO:DIPHOSPHATE MG:MAGNESIUM ION PRP:1-O-PYROPHOSPHONO-5-O-PHOSPHONO-ALPHA-D-RIBOFURANOSE | |||
| 3qr9 | [A2] | [A2] | [A2] | 1.87 | GOL:GLYCEROL | |||
| 3qs8 | [A2] | [A2] | [A2] | 2 | 17D:2-BENZYLBENZOIC ACID MG:MAGNESIUM ION PRP:1-O-PYROPHOSPHONO-5-O-PHOSPHONO-ALPHA-D-RIBOFURANOSE | |||
| 3qsa | [A2] | [A2] | [A2] | 2.18 | MG:MAGNESIUM ION PRP:1-O-PYROPHOSPHONO-5-O-PHOSPHONO-ALPHA-D-RIBOFURANOSE TA7:4,4,4-TRIFLUORO-1-(4-METHOXYPHENYL)BUTANE-1,3-DIONE | |||
| 3r6c | [A] | [A] | [A] | 1.83 | 17N:8-METHOXYPHENANTHRO[3,4-D][1,3]DIOXOLE-5,6-DICARBOXYLICACID GOL:GLYCEROL MG:MAGNESIUM ION PRP:1-O-PYROPHOSPHONO-5-O-PHOSPHONO-ALPHA-D-RIBOFURANOSE | |||
| 3r88 | [A2] | [A2] | [A2] | 1.73 | 14F:2-AMINO-4,5-DIMETHOXYBENZOIC ACID GOL:GLYCEROL MG:MAGNESIUM ION PRP:1-O-PYROPHOSPHONO-5-O-PHOSPHONO-ALPHA-D-RIBOFURANOSE | |||
| 3twp | [A2] | [A2] | [A2] | 1.83 | GOL:GLYCEROL MG:MAGNESIUM ION PRP:1-O-PYROPHOSPHONO-5-O-PHOSPHONO-ALPHA-D-RIBOFURANOSE SAL:2-HYDROXYBENZOIC ACID | |||
| 3uu1 | [A] | [A] | [A] | 1.82 | 14B:2-AMINO-3,5-DIMETHYLBENZOIC ACID MG:MAGNESIUM ION PRP:1-O-PYROPHOSPHONO-5-O-PHOSPHONO-ALPHA-D-RIBOFURANOSE | |||
| 4ead | [A2] | [A2] | [A2] | 1.5 | 0NP:2___sq___,3___sq___-DIDEOXY-2___sq___-FLUORO-3___sq___-TRIAZA-1,2-DIEN-2-IUM-1-YLURIDINE GOL:GLYCEROL SO4:SULFATE ION | |||
| 4eaf | [A2] | [A2] | [A2] | 1.55 | GOL:GLYCEROL SO4:SULFATE ION | |||
| 4ga4 | [A2] | [A2] | [A2] | 3.51 | PO4:PHOSPHATE ION | |||
| 4ga5 | [A2] | [A2] | [A2] | 3.25 | ||||
| 4ga6 | [A2] | [A2] | [A2] | 2.21 | AMP:ADENOSINE MONOPHOSPHATE SO4:SULFATE ION | |||
| 4giu | [A2] | [A2] | [A2] | 1.67 | 636:2-[(2-CARBOXY-5-METHYLPHENYL)AMINO]-3-METHYLBENZOICACID DMS:DIMETHYL SULFOXIDE GOL:GLYCEROL MG:MAGNESIUM ION PRP:1-O-PYROPHOSPHONO-5-O-PHOSPHONO-ALPHA-D-RIBOFURANOSE | |||
| 4gkm | [A2] | [A2] | [A2] | 1.67 | 683:2-[(2-CARBOXYPHENYL)AMINO]-5-METHYLBENZOIC ACID DMS:DIMETHYL SULFOXIDE GOL:GLYCEROL MG:MAGNESIUM ION PRP:1-O-PYROPHOSPHONO-5-O-PHOSPHONO-ALPHA-D-RIBOFURANOSE | |||
| 4gtn | [A2] | [A2] | [A2] | 2.03 | ||||
| 4hkm | [A2] | [A2] | [A2] | 1.95 | CXS:3-CYCLOHEXYL-1-PROPYLSULFONIC ACID GOL:GLYCEROL MSE:SELENOMETHIONINE PO4:PHOSPHATE ION | |||
| 4ij1 | [A2] | [A2] | [A2] | 1.79 | 17C:2,2___sq___-IMINODIBENZOIC ACID GOL:GLYCEROL IMD:IMIDAZOLE | |||
| 4lhm | [A2] | [A2] | [A2] | 1.52 | AZZ:3___sq___-AZIDO-3___sq___-DEOXYTHYMIDINE GOL:GLYCEROL SO4:SULFATE ION | |||
| 4m0r | [A2] | [A2] | [A2] | 1.96 | 644:2,6-BIS[(2-CARBOXYPHENYL)AMINO]BENZOIC ACID DMS:DIMETHYL SULFOXIDE GOL:GLYCEROL IMD:IMIDAZOLE | |||
| 4muo | [A2] | [A2] | [A2] | 1.94 | ||||
| 4n5v | [A2] | [A2] | [A2] | 1.9 | FA0:2-AMINO-4-FLUOROBENZOIC ACID GOL:GLYCEROL MG:MAGNESIUM ION PRP:1-O-PYROPHOSPHONO-5-O-PHOSPHONO-ALPHA-D-RIBOFURANOSE | |||
| 4n8q | [A2] | [A2] | [A2] | 2.08 | FA0:2-AMINO-4-FLUOROBENZOIC ACID | |||
| 4n93 | [A2] | [A2] | [A2] | 2.03 | 6M1:2-AMINO-6-METHYLBENZOIC ACID GOL:GLYCEROL MG:MAGNESIUM ION PRP:1-O-PYROPHOSPHONO-5-O-PHOSPHONO-ALPHA-D-RIBOFURANOSE | |||
| 4owm | [A2] | [A2] | [A2] | 1.99 | 3F0:2-AZANYL-3-FLUORANYL-BENZOIC ACID GOL:GLYCEROL IMD:IMIDAZOLE MG:MAGNESIUM ION PRP:1-O-PYROPHOSPHONO-5-O-PHOSPHONO-ALPHA-D-RIBOFURANOSE | |||
| 4own | [A2] | [A2] | [A2] | 2.11 | 5RG:2-AMINO-5-FLUOROBENZOIC ACID GOL:GLYCEROL IMD:IMIDAZOLE MG:MAGNESIUM ION POP:PYROPHOSPHATE 2- PRP:1-O-PYROPHOSPHONO-5-O-PHOSPHONO-ALPHA-D-RIBOFURANOSE | |||
| 4owo | [A2] | [A2] | [A2] | 1.99 | 6F0:2-AZANYL-6-FLUORANYL-BENZOIC ACID GOL:GLYCEROL IMD:IMIDAZOLE MG:MAGNESIUM ION PRP:1-O-PYROPHOSPHONO-5-O-PHOSPHONO-ALPHA-D-RIBOFURANOSE | |||
| 4owq | [A2] | [A2] | [A2] | 1.89 | 3M0:2-AZANYL-3-METHYL-BENZOIC ACID GOL:GLYCEROL IMD:IMIDAZOLE MG:MAGNESIUM ION PRP:1-O-PYROPHOSPHONO-5-O-PHOSPHONO-ALPHA-D-RIBOFURANOSE | |||
| 4ows | [A2] | [A2] | [A2] | 2.43 | 4M0:2-AZANYL-4-METHYL-BENZOIC ACID IMD:IMIDAZOLE POP:PYROPHOSPHATE 2- | |||
| 4owu | [A2] | [A2] | [A2] | 1.89 | 5M0:2-AZANYL-5-METHYL-BENZOIC ACID GOL:GLYCEROL IMD:IMIDAZOLE MG:MAGNESIUM ION PRP:1-O-PYROPHOSPHONO-5-O-PHOSPHONO-ALPHA-D-RIBOFURANOSE | |||
| 4owv | [A2] | [A2] | [A2] | 1.9 | BE2:2-AMINOBENZOIC ACID GOL:GLYCEROL PO4:PHOSPHATE ION | |||
| 4x46 | [A2] | [A2] | [A2] | 2.2 | EDO:1,2-ETHANEDIOL SO4:SULFATE ION | |||
| 4x58 | [A2] | [A2] | [A2] | 1.75 | GOL:GLYCEROL IMD:IMIDAZOLE MG:MAGNESIUM ION MLT:D-MALATE PRP:1-O-PYROPHOSPHONO-5-O-PHOSPHONO-ALPHA-D-RIBOFURANOSE | |||
| 4x59 | | [A2] | [A2] | [A2] | 1.8 | GOL:GLYCEROL IMD:IMIDAZOLE MG:MAGNESIUM ION PRP:1-O-PYROPHOSPHONO-5-O-PHOSPHONO-ALPHA-D-RIBOFURANOSE | ||
| 4x5a | | [A2] | [A2] | [A2] | 1.93 | GOL:GLYCEROL | ||
| 4x5b | | [A2] | [A2] | [A2] | 2.47 | MG:MAGNESIUM ION PRP:1-O-PYROPHOSPHONO-5-O-PHOSPHONO-ALPHA-D-RIBOFURANOSE | ||
| 4x5c | | [A2] | [A2] | [A2] | 2.33 | MG:MAGNESIUM ION POP:PYROPHOSPHATE 2- PRP:1-O-PYROPHOSPHONO-5-O-PHOSPHONO-ALPHA-D-RIBOFURANOSE | ||
| 4x5d | [A2] | [A2] | [A2] | 2.3 | BE2:2-AMINOBENZOIC ACID GOL:GLYCEROL IMD:IMIDAZOLE | |||
| 4x5e | [A2] | [A2] | [A2] | 1.77 | BE2:2-AMINOBENZOIC ACID GOL:GLYCEROL MG:MAGNESIUM ION POP:PYROPHOSPHATE 2- | |||
| 4xr5 | [A2] | [A2] | [A2] | 2.05 | CL:CHLORIDE ION PEG:DI(HYDROXYETHYL)ETHER PGE:TRIETHYLENE GLYCOL | |||
| 4yek | [A2] | [A2] | [A2] | 2.55 | EDO:1,2-ETHANEDIOL GOL:GLYCEROL PGE:TRIETHYLENE GLYCOL SO4:SULFATE ION THM:THYMIDINE | |||
| 4yi7 | [A2] | [A2] | [A2] | 1.85 | BE2:2-AMINOBENZOIC ACID | |||
| 4yyy | [A2] | [A2] | [A2] | 2.43 | CIT:CITRIC ACID PGE:TRIETHYLENE GLYCOL URI:URIDINE | |||
| 4zof | [A2] | [A2] | [A2] | 1.8 | 59L:2-[(2-CARBOXY-5-NITROPHENYL)AMINO]-3-METHYLBENZOIC ACID IMD:IMIDAZOLE MG:MAGNESIUM ION PO4:PHOSPHATE ION PRP:1-O-PYROPHOSPHONO-5-O-PHOSPHONO-ALPHA-D-RIBOFURANOSE | |||
| 4zoj | [A2] | [A2] | [A2] | 1.96 | 61L:4-METHYL-2-{[2-METHYL-6-(METHYLSULFANYL)PHENYL]AMINO}BENZOIC ACID IMD:IMIDAZOLE MG:MAGNESIUM ION PO4:PHOSPHATE ION PRP:1-O-PYROPHOSPHONO-5-O-PHOSPHONO-ALPHA-D-RIBOFURANOSE | |||
| 4zok | [A2] | [A2] | [A2] | 2.34 | 62L:4-METHYL-2-{[2-METHYL-6-(METHYLSULFONYL)PHENYL]AMINO}BENZOIC ACID MG:MAGNESIUM ION PRP:1-O-PYROPHOSPHONO-5-O-PHOSPHONO-ALPHA-D-RIBOFURANOSE | |||
| 4ztv | [A2] | [A2] | [A2] | 2.01 | TA7:4,4,4-TRIFLUORO-1-(4-METHOXYPHENYL)BUTANE-1,3-DIONE | |||
| 5bne | [A2] | [A2] | [A2] | 2.15 | 7P3:2-[(2-CARBOXYPHENYL)AMINO]-5-[(5-PHOSPHONOPENTYL)OXY]BENZOIC ACID IMD:IMIDAZOLE | |||
| 5bo2 | [A2] | [A2] | [A2] | 2 | 7P1:2-[(2-CARBOXYPHENYL)AMINO]-5-(3-PHOSPHONOPROPOXY)BENZOIC ACID IMD:IMIDAZOLE | |||
| 5bo3 | [A2] | [A2] | [A2] | 1.75 | 7P2:2-[(2-CARBOXYPHENYL)AMINO]-5-(4-PHOSPHONOBUTOXY)BENZOICACID IMD:IMIDAZOLE | |||
| 5byt | [A2] | [A2] | [A2] | 2 | MG:MAGNESIUM ION PRP:1-O-PYROPHOSPHONO-5-O-PHOSPHONO-ALPHA-D-RIBOFURANOSE | |||
| 5c1r | [A2] | [A2] | [A2] | 1.8 | 51N:5-O-[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]-1-O-PHOSPHONO-ALPHA-D-RIBOFURANOSE GOL:GLYCEROL MG:MAGNESIUM ION | |||
| 5c2l | [A2] | [A2] | [A2] | 2.01 | IMD:IMIDAZOLE MG:MAGNESIUM ION | |||
| 5c7s | [A2] | [A2] | [A2] | 2.1 | MN:MANGANESE (II) ION PRP:1-O-PYROPHOSPHONO-5-O-PHOSPHONO-ALPHA-D-RIBOFURANOSE | |||
| 5ep8 | [A2] | [A2] | [A2] | 2.66 | NA:SODIUM ION SO4:SULFATE ION | |||
| 5ey3 | [A2] | [A2] | [A2] | 1.91 | CTN:4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE EDO:1,2-ETHANEDIOL GOL:GLYCEROL SO4:SULFATE ION | |||
| 5noe | [A2] | [A2] | [A2] | 1.91 | ||||
| 5nof | [A] | [A] | [A] | 2.42 | CL:CHLORIDE ION NA:SODIUM ION ZN:ZINC ION | |||
| 5oln | [A] | [A] | [A] | 1.88 | EDO:1,2-ETHANEDIOL IMD:IMIDAZOLE SO4:SULFATE ION | |||
*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
