- Class: 3
- Architecture: 3.40:3-Layer(aba) Sandwich
- Topology: 3.40.50:Rossmann fold
- Homology: 3.40.50.960:Lumazine/riboflavin synthase
PDB Entries
PDB ID | OPM | Mutant | Chain Formula | Resolution | HETNAM | |||
---|---|---|---|---|---|---|---|---|
Amino Acid sequence | SCOPe Family Level | CATH Homology Level | ||||||
1c2y | [A20] | [A20] | [A20] | 3.3 | LMZ:5-NITROSO-6-RIBITYL-AMINO-2,4(1H,3H)-PYRIMIDINEDIONE | |||
1c41 | [A5] | [A5] | [A5] | 3.1 | LMZ:5-NITROSO-6-RIBITYL-AMINO-2,4(1H,3H)-PYRIMIDINEDIONE SO4:SULFATE ION | |||
1di0 | [A5] | [A5] | [A5] | 2.7 | PO4:PHOSPHATE ION | |||
1ejb | [A5] | [A5] | [A5] | 1.85 | INJ:5-(6-D-RIBITYLAMINO-2,4-DIHYDROXYPYRIMIDIN-5-YL)-1-PENTYL-PHOSPHONIC ACID | |||
1hqk | [A60] | [A60] | [A60] | 1.6 | ||||
1kyv | [A5] | [A5] | [A5] | 2.4 | PO4:PHOSPHATE ION RBF:RIBOFLAVIN | |||
1kyx | [A5] | [A5] | [A5] | 2.6 | CRM:3-[8-((2S,3S,4R)-2,3,4,5-TETRAHYDROXYPENTYL)-2,4,7-TRIOXO-1,3,8-TRIHYDROPTERIDIN-6-YL]PROPANOIC ACID PO4:PHOSPHATE ION | |||
1kyy | [A5] | [A5] | [A5] | 2.4 | INI:5-NITRO-6-RIBITYL-AMINO-2,4(1H,3H)-PYRIMIDINEDIONE PO4:PHOSPHATE ION | |||
1kz1 | [A5] | [A5] | [A5] | 2 | ||||
1kz4 | [A5] | [A5] | [A5] | 3.1 | PO4:PHOSPHATE ION | |||
1kz6 | [A5] | [A5] | [A5] | 2.7 | PO4:PHOSPHATE ION | |||
1kz9 | [A5] | [A5] | [A5] | 3.1 | PO4:PHOSPHATE ION | |||
1nqu | [A60] | [A60] | [A60] | 1.75 | PO4:PHOSPHATE ION RDL:6,7-DIOXO-5H-8-RIBITYLAMINOLUMAZINE | |||
1nqv | [A60] | [A60] | [A60] | 2.05 | LMZ:5-NITROSO-6-RIBITYL-AMINO-2,4(1H,3H)-PYRIMIDINEDIONE PO4:PHOSPHATE ION | |||
1nqw | [A60] | [A60] | [A60] | 2.2 | 5YL:5-(6-D-RIBITYLAMINO-2,4(1H,3H)PYRIMIDINEDIONE-5-YL)PENTYL-1-PHOSPHONIC ACID | |||
1nqx | [A60] | [A60] | [A60] | 1.82 | PO4:PHOSPHATE ION RLP:3-(7-HYDROXY-8-RIBITYLLUMAZINE-6-YL) PROPIONIC ACID | |||
1rvv | [A30] | [A30] | [A30] | 2.4 | INI:5-NITRO-6-RIBITYL-AMINO-2,4(1H,3H)-PYRIMIDINEDIONE PO4:PHOSPHATE ION | |||
1t13 | [A10] | [A10] | [A10] | 2.9 | INI:5-NITRO-6-RIBITYL-AMINO-2,4(1H,3H)-PYRIMIDINEDIONE PO4:PHOSPHATE ION | |||
1w19 | [A10] | [A10] | [A10] | 2 | ACY:ACETIC ACID D1D:(4S,5S)-1,2-DITHIANE-4,5-DIOL DTU:(2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL DTV:(2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL K:POTASSIUM ION T1P:3-{2,6,8-TRIOXO-9-[(2R,3S,4R)-2,3,4,5-TETRAHYDROXYPENTYL]-1,2,3,6,8,9-HEXAHYDRO-7H-PURIN-7-YL}PROPYL DIHYDROGEN PHOSPHATE T2P:3-{2,6,8-TRIOXO-9-[(2S,3R,4R)-2,3,4,5-TETRAHYDROXYPENTYL]-1,2,3,6,8,9-HEXAHYDRO-7H-PURIN-7-YL}PROPYL DIHYDROGEN PHOSPHATE T4P:3-{2,6,8-TRIOXO-9-[(2R,3R,4R)-2,3,4,5-TETRAHYDROXYPENTYL]-1,2,3,6,8,9-HEXAHYDRO-7H-PURIN-7-YL}PROPYL DIHYDROGEN PHOSPHATE T5P:3-{2,6,8-TRIOXO-9-[(2S,3S,4R)-2,3,4,5-TETRAHYDROXYPENTYL]-1,2,3,6,8,9-HEXAHYDRO-7H-PURIN-7-YL}PROPYL DIHYDROGEN PHOSPHATE | |||
1w29 | [A10] | [A10] | [A10] | 2.3 | ACY:ACETIC ACID D1D:(4S,5S)-1,2-DITHIANE-4,5-DIOL K:POTASSIUM ION TS0:4-{2,6,8-TRIOXO-9-[(2S,3R,4R)-2,3,4,5-TETRAHYDROXYPENTYL]-1,2,3,6,8,9-HEXAHYDRO-7H-PURIN-7-YL}BUTYL DIHYDROGEN PHOSPHATE TS1:4-{2,6,8-TRIOXO-9-[(2R,3S,4R)-2,3,4,5-TETRAHYDROXYPENTYL]-1,2,3,6,8,9-HEXAHYDRO-7H-PURIN-7-YL}BUTYL DIHYDROGEN PHOSPHATE | |||
1xn1 | [A10] | [A10] | [A10] | 3.05 | NA:SODIUM ION PO4:PHOSPHATE ION SO4:SULFATE ION | |||
1zis | [A5] | [A5] | [A5] | 2.9 | INI:5-NITRO-6-RIBITYL-AMINO-2,4(1H,3H)-PYRIMIDINEDIONE PO4:PHOSPHATE ION | |||
2a57 | [A5] | [A5] | [A5] | 2.75 | CRM:3-[8-((2S,3S,4R)-2,3,4,5-TETRAHYDROXYPENTYL)-2,4,7-TRIOXO-1,3,8-TRIHYDROPTERIDIN-6-YL]PROPANOIC ACID PO4:PHOSPHATE ION | |||
2a58 | [A5] | [A5] | [A5] | 2.8 | PO4:PHOSPHATE ION RBF:RIBOFLAVIN | |||
2a59 | [A5] | [A5] | [A5] | 2.7 | LMZ:5-NITROSO-6-RIBITYL-AMINO-2,4(1H,3H)-PYRIMIDINEDIONE PO4:PHOSPHATE ION | |||
2b98 | [A5] | [A5] | [A5] | 2.3 | ||||
2b99 | [A5] | [A5] | [A5] | 2.22 | RDL:6,7-DIOXO-5H-8-RIBITYLAMINOLUMAZINE | |||
2c92 | [A5] | [A5] | [A5] | 1.6 | DTU:(2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL K:POTASSIUM ION MPD:(4S)-2-METHYL-2,4-PENTANEDIOL TP6:3-(1,3,7-TRIHYDRO-9-D-RIBITYL-2,6,8-PURINETRIONE-7-YL)1-PHOSPHATE | |||
2c94 | [A5] | [A5] | [A5] | 1.9 | K:POTASSIUM ION TSF:3-(1,3,7-TRIHYDRO-9-D-RIBITYL-2,6,8-PURINETRIONE-7-YL)1,1 DIFLUOROPENTANE-1-PHOSPHATE | |||
2c97 | [A5] | [A5] | [A5] | 2 | ACT:ACETATE ION DTD:DITHIANE DIOL JCL:4-(6-CHLORO-2,4-DIOXO-1,2,3,4-TETRAHYDROPYRIMIDIN-5-YL)BUTYL PHOSPHATE K:POTASSIUM ION MPD:(4S)-2-METHYL-2,4-PENTANEDIOL | |||
2c9b | [A5] | [A5] | [A5] | 2.75 | K:POTASSIUM ION MPD:(4S)-2-METHYL-2,4-PENTANEDIOL PO4:PHOSPHATE ION PUG:3-(1,3,7-TRIHYDRO-9-D-RIBITYL-2,6,8-PURINETRIONE-7-YL) | |||
2c9d | [A5] | [A5] | [A5] | 2.8 | K:POTASSIUM ION MPD:(4S)-2-METHYL-2,4-PENTANEDIOL PHR:3-(1,3,7-TRIHYDRO-9-D-RIBITYL-2,6,8-PURINETRIONE-7-YL )HEXANE 1-PHOSPHATE | |||
2f59 | [A5] | [A5] | [A5] | 2.3 | CA:CALCIUM ION INI:5-NITRO-6-RIBITYL-AMINO-2,4(1H,3H)-PYRIMIDINEDIONE | |||
2i0f | [A5] | [A5] | [A5] | 2.22 | CA:CALCIUM ION | |||
2jfb | [A5] | [A5] | [A5] | 2.5 | MPD:(4S)-2-METHYL-2,4-PENTANEDIOL PO4:PHOSPHATE ION | |||
2o6h | [A5] | [A5] | [A5] | 2.7 | CA:CALCIUM ION INI:5-NITRO-6-RIBITYL-AMINO-2,4(1H,3H)-PYRIMIDINEDIONE | |||
2obx | [A10] | [A10] | [A10] | 2.53 | INI:5-NITRO-6-RIBITYL-AMINO-2,4(1H,3H)-PYRIMIDINEDIONE PO4:PHOSPHATE ION | |||
2vi5 | [A5] | [A5] | [A5] | 2.3 | K:POTASSIUM ION PO4:PHOSPHATE ION Y19:1-DEOXY-1-{[(5S)-2,6-DIOXO-5-(PROPANOYLAMINO)-1,2,5,6-TETRAHYDROPYRIMIDIN-4-YL]AMINO}-D-RIBITOL | |||
3mk3 | [A60] | [A60] | [A60] | 3.57 | SO4:SULFATE ION | |||
3nq4 | [A60] | [A60] | [A60] | 3.5 | SO4:SULFATE ION | |||
4j07 | [A5] | [A5] | [A5] | 1.95 | NA:SODIUM ION SO4:SULFATE ION | |||
4kq6 | [A5] | [A5] | [A5] | 2.24 | DLZ:1-DEOXY-1-(6,7-DIMETHYL-2,4-DIOXO-3,4-DIHYDROPTERIDIN-8(2H)-YL)-D-RIBITOL GOL:GLYCEROL SO4:SULFATE ION | |||
5im4 | [A60B60] | [A60B60] | [A60B60] | 3.5 | ||||
5im5 | [A60B60] | [A60B60] | [A60B60] | 3.7 | ||||
5mpp | [A60] | [A60] | [A60] | 3.94 |
*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