Luciferin 4-monooxygenase
Photinus pyralis
State in the Current Structure
| Assembly | Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Associated Components | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|
| 1 | Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count | Chain A; UniProt 1–550 | Not recorded | 5J4 2-[6-(cyclobuta-1,3-dien-1-ylamino)-1,3-benzothiazol-2-yl]-1,3-thiazol-4-ol × 1 | X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 8;293 K;Li2SO4, PEG8000, Tris | Resolution 2.30 Å R-free 0.228 |
Other States of the Same Protein in the Database
Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.
| Other PDB | Difference from Current Entry 5DWV | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 1BA3 FIREFLY LUCIFERASE IN COMPLEX WITH BROMOFORM Deposited 1998-04-21 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
1–550(550 aa)
|
Not recorded | MBR TRIBROMOMETHANE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
microbatch under oil;pH 7.8;283 K;2 MICROLITRE OF LUCIFERASE (20 MG/ML) IN 0.2M AMMONIUM SULFATE, 0.001M EDTA, 0.001M DTT, 10% GLYCEROL, 25% ETHYLENE GLYCOL, 0.025M TRIS-HCL PH7.8 + 2 MICROLITRE 0.5M LITHIUM SULFATE, 26% PEG 8000, 0.1M TRIS-HCL PH7.8 AT 10 DEGREES CELSIUS IN MICROBATCH UNDER OIL., microbatch under oil, temperature 283K
|
Resolution 2.20 Å R-free 0.239 |
| 1LCI FIREFLY LUCIFERASE Deposited 1996-06-01 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
1–550(550 aa)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
microbatch under oil;pH 7.8;283 K;2 MICROLITRE OF LUCIFERASE (20 MG/ML) IN 0.2M AMMONIUM SULFATE, 0.001M EDTA, 0.001M DTT, 10% GLYCEROL, 25% ETHYLENE GLYCOL, 0.025M TRIS-HCL PH7.8 + 2 MICROLITRE 0.5M LITHIUM SULFATE, 26% PEG 8000, 0.1M TRIS-HCL PH7.8 AT 10 DEGREES CELSIUS IN MICROBATCH UNDER OIL. CRYOPROTECTANT SOLUTION: 8% PEG 8000, 10% GLYCEROL, 12.5% ETHYLENE GLYCOL, 0.1M TRIS-HCL PH7.8, microbatch under oil, temperature 283K
|
Resolution 2.00 Å R-free 0.265 |
| 3IEP Firefly luciferase apo structure (P41 form) Deposited 2009-07-23 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
1–550(550 aa)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION;pH 8.5;277 K;30% PEG 1500, 8% MPD, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, temperature 277K
|
Resolution 2.10 Å R-free 0.221 |
| 3IER Firefly luciferase apo structure (P41 form) with PEG 400 bound Deposited 2009-07-23 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
1–550(550 aa)
|
Not recorded | PG4 TETRAETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION;pH 8.5;277 K;25% PEG 400, 20% PEG 3350, 0.1M MgCl2, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, temperature 277K
|
Resolution 2.05 Å R-free 0.225 |
| 3IES Firefly luciferase inhibitor complex Deposited 2009-07-23 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
1–550(550 aa)
|
Not recorded | M24 5'-O-[(R)-[({3-[5-(2-fluorophenyl)-1,2,4-oxadiazol-3-yl]phenyl}carbonyl)oxy](hydroxy)phosphoryl]adenosine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION;pH 8.5;277 K;30% PEG 1500, 8% MPD, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, temperature 277K
|
Resolution 2.00 Å R-free 0.218 |
| 3RIX 1.7A resolution structure of a firefly luciferase-Aspulvinone J inhibitor complex Deposited 2011-04-14 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
1–550(550 aa)
|
Not recorded | 923 (5Z)-4-hydroxy-3-[(2R)-2-(2-hydroxypropan-2-yl)-2,3-dihydro-1-benzofuran-5-yl]-5-{[(2R)-2-(2-hydroxypropan-2-yl)-2,3-dihydro-1-benzofuran-5-yl]methylidene}furan-2(5H)-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION;pH 8.5;277 K;25% (v/v) PEG 400, 20% (v/v) PEG 3350, 0.1 M MgCl2, 0.1 M Tris, pH 8.5, vapor diffusion, temperature 277K
|
Resolution 1.70 Å R-free 0.218 |
| 4E5D 2.2A resolution structure of a firefly luciferase-benzothiazole inhibitor complex Deposited 2012-03-14 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
1–550(550 aa)
|
Not recorded | 0NJ 2-(2-fluorophenyl)-6-methoxy-1,3-benzothiazole × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION;pH 8.5;277 K;25% (v/v) PEG 400, 20% (v/v) PEG 3350, 0.1 M MgCl2, 0.1 M Tris, pH 8.5, vapor diffusion, temperature 277K
|
Resolution 2.20 Å R-free 0.232 |
| 4G36 Photinus pyralis luciferase in the adenylate-forming conformation bound to DLSA Deposited 2012-07-13 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
1–550(550 aa)
|
Not recorded | SLU 5'-O-[N-(DEHYDROLUCIFERYL)-SULFAMOYL] ADENOSINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;300 mM Na/K Tartrate, 20% PEG 6000, 100 mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.62 Å R-free 0.238 |
| 4G36 Photinus pyralis luciferase in the adenylate-forming conformation bound to DLSA Deposited 2012-07-13 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain B
1–550(550 aa)
|
Not recorded | SLU 5'-O-[N-(DEHYDROLUCIFERYL)-SULFAMOYL] ADENOSINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;300 mM Na/K Tartrate, 20% PEG 6000, 100 mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.62 Å R-free 0.238 |
| 4G37 Structure of cross-linked firefly luciferase in second catalytic conformation Deposited 2012-07-13 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
1–550(550 aa)
|
Mutation:C82S, I108C, T214A, A215L, C216A, I232A, C258S, F295L, E354K, C391S, Y447C | SLU 5'-O-[N-(DEHYDROLUCIFERYL)-SULFAMOYL] ADENOSINE × 1 XLX 4,4'-(ethylenediimino)bis[4-oxobutyrate] × 1 SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP;pH 8.5;273 K;30 % PEG 4000, 50 mM NaCl, 50 mM HEPPS, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 273K
|
Resolution 2.40 Å R-free 0.259 |
| 4G37 Structure of cross-linked firefly luciferase in second catalytic conformation Deposited 2012-07-13 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain B
1–550(550 aa)
|
Mutation:C82S, I108C, T214A, A215L, C216A, I232A, C258S, F295L, E354K, C391S, Y447C | SLU 5'-O-[N-(DEHYDROLUCIFERYL)-SULFAMOYL] ADENOSINE × 1 XLX 4,4'-(ethylenediimino)bis[4-oxobutyrate] × 1 SO4 SULFATE ION × 2 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP;pH 8.5;273 K;30 % PEG 4000, 50 mM NaCl, 50 mM HEPPS, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 273K
|
Resolution 2.40 Å R-free 0.259 |
| 5DV9 Crystal structure of the Luciferase Deposited 2015-09-21 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
1–550(550 aa)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION;pH 8;293 K;Li2SO4, PEG 8000, Tris
|
Resolution 2.40 Å R-free 0.241 |
| 5GYZ luciferase AMP/7-cy-L complex Deposited 2016-09-26 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
4–438(435 aa)
Fragment:UNP residues 4-438
|
Not recorded | 7BV (4S)-2-[6-(azepan-1-yl)-1,3-benzothiazol-2-yl]-4,5-dihydro-1,3-thiazole-4-carboxylic acid × 1 AMP ADENOSINE MONOPHOSPHATE × 1 PEG DI(HYDROXYETHYL)ETHER × 1 GOL GLYCEROL × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION;293 K;Sodium malonate, PEG3350
|
Resolution 2.40 Å R-free 0.227 |
| 5GZ2 luciferase complex with 7-cy-L Deposited 2016-09-26 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
3–438(436 aa)
Fragment:UNP residues 3-438
|
Not recorded | 7BV (4S)-2-[6-(azepan-1-yl)-1,3-benzothiazol-2-yl]-4,5-dihydro-1,3-thiazole-4-carboxylic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP;290 K;Sodium malonate , PEG3350
|
Resolution 2.00 Å R-free 0.239 |
| 5KYT Structure of Photinus pyralis Luciferase red light emitting variant Deposited 2016-07-22 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
1–550(550 aa)
|
Mutation:S284T | SLU 5'-O-[N-(DEHYDROLUCIFERYL)-SULFAMOYL] ADENOSINE × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP;pH 7.4;293 K;23 % PEG 8000, 300 mM Na/K tartrate, 1.00 mM Tris
|
Resolution 2.00 Å R-free 0.218 |
| 5KYT Structure of Photinus pyralis Luciferase red light emitting variant Deposited 2016-07-22 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain B
1–550(550 aa)
|
Mutation:S284T | SLU 5'-O-[N-(DEHYDROLUCIFERYL)-SULFAMOYL] ADENOSINE × 1 EDO 1,2-ETHANEDIOL × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP;pH 7.4;293 K;23 % PEG 8000, 300 mM Na/K tartrate, 1.00 mM Tris
|
Resolution 2.00 Å R-free 0.218 |
| 5KYV Structure of Photinus pyralis Luciferase green shifted light emitting variant Deposited 2016-07-22 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
1–550(550 aa)
|
Mutation:V241I, G246A, F250S | SLU 5'-O-[N-(DEHYDROLUCIFERYL)-SULFAMOYL] ADENOSINE × 1 TLA L(+)-TARTARIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP;pH 7.4;293 K;23 % PEG 8000, 200 mM Na/K tartrate, 1.00 mM Tris
|
Resolution 2.50 Å R-free 0.247 |
| 5KYV Structure of Photinus pyralis Luciferase green shifted light emitting variant Deposited 2016-07-22 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain B
1–550(550 aa)
|
Mutation:V241I, G246A, F250S | SLU 5'-O-[N-(DEHYDROLUCIFERYL)-SULFAMOYL] ADENOSINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP;pH 7.4;293 K;23 % PEG 8000, 200 mM Na/K tartrate, 1.00 mM Tris
|
Resolution 2.50 Å R-free 0.247 |
| 5WYS luciferase with inhibitor 3i Deposited 2017-01-15 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
1–550(550 aa)
|
Not recorded | 7V6 5-[(3R)-3-(4-boranylphenyl)-3-oxidanyl-propyl]-2-oxidanyl-benzoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION;pH 8;293 K;0.5 M Li2SO4, 15% PEG8000, 0.1 M Tris
|
Resolution 3.00 Å R-free 0.270 |
| 6HPS Near-infrared dual bioluminescence imaging in vivo using infra-luciferin Deposited 2018-09-21 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
4–546(543 aa)
|
Not recorded | GKH [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[[2-[(~{E})-2-(6-oxidanyl-1,3-benzothiazol-2-yl)ethenyl]-1,3-thiazol-4-yl]carbonyl]sulfamate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP;pH 7;278 K;150 mM ammonium sulfate, 50 mM HEPES pH 7.0, 2% PEG 1000
|
Resolution 3.10 Å R-free 0.333 |
| 6HPS Near-infrared dual bioluminescence imaging in vivo using infra-luciferin Deposited 2018-09-21 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain B
4–546(543 aa)
|
Not recorded | GKH [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[[2-[(~{E})-2-(6-oxidanyl-1,3-benzothiazol-2-yl)ethenyl]-1,3-thiazol-4-yl]carbonyl]sulfamate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP;pH 7;278 K;150 mM ammonium sulfate, 50 mM HEPES pH 7.0, 2% PEG 1000
|
Resolution 3.10 Å R-free 0.333 |
| 6Q2M Crystal structure of Photinus pyralis Luciferase Pps6 mutant in complex with DLSA Deposited 2019-08-08 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
1–550(550 aa)
|
Mutation:T214N, A222C, Y255F, S276T, H332N, E354N | SO4 SULFATE ION × 1 DYD (2S,5S)-hexane-2,5-diol × 2 EDO 1,2-ETHANEDIOL × 16 SLU 5'-O-[N-(DEHYDROLUCIFERYL)-SULFAMOYL] ADENOSINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP;pH 8.5;293.15 K;0.05M EPPS pH 8.5, 25% PEG4000, 2% 2,5 Hexanediol
|
Resolution 2.75 Å R-free 0.218 |
| 6Q2M Crystal structure of Photinus pyralis Luciferase Pps6 mutant in complex with DLSA Deposited 2019-08-08 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain B
1–550(550 aa)
|
Mutation:T214N, A222C, Y255F, S276T, H332N, E354N | SO4 SULFATE ION × 3 EDO 1,2-ETHANEDIOL × 7 SLU 5'-O-[N-(DEHYDROLUCIFERYL)-SULFAMOYL] ADENOSINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP;pH 8.5;293.15 K;0.05M EPPS pH 8.5, 25% PEG4000, 2% 2,5 Hexanediol
|
Resolution 2.75 Å R-free 0.218 |
| 6Q2M Crystal structure of Photinus pyralis Luciferase Pps6 mutant in complex with DLSA Deposited 2019-08-08 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain C
1–550(550 aa)
|
Mutation:T214N, A222C, Y255F, S276T, H332N, E354N | SO4 SULFATE ION × 2 DYD (2S,5S)-hexane-2,5-diol × 2 EDO 1,2-ETHANEDIOL × 16 SLU 5'-O-[N-(DEHYDROLUCIFERYL)-SULFAMOYL] ADENOSINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP;pH 8.5;293.15 K;0.05M EPPS pH 8.5, 25% PEG4000, 2% 2,5 Hexanediol
|
Resolution 2.75 Å R-free 0.218 |
17 other PDB entries and 24 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | LUCI_PHOPY |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A; PDBConstruct 24–573; UniProt 1–550 |