5b0u

Crystal structure of the mutated 19 kDa protein of Oplophorus luciferase (nanoKAZ)

Method: X-RAY DIFFRACTION D_max: 110.1 Å Quality: REASONABLE

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Oplophorus-luciferin 2-monooxygenase catalytic subunit

Oplophorus gracilirostris

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 28–196	Mutation：A4E, Q11R, Q18L, L27V, A33N, K43R, V44I, A54I, F68D, L72Q, M75K,I90V, P115E, Q124K, Y138I, N166R	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；1.1 M di-ammonium tartrate	Resolution 1.71 Å R-free 0.226
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 28–196	Mutation：A4E, Q11R, Q18L, L27V, A33N, K43R, V44I, A54I, F68D, L72Q, M75K,I90V, P115E, Q124K, Y138I, N166R	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；1.1 M di-ammonium tartrate	Resolution 1.71 Å R-free 0.226

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 5B0U	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5IBO 1.95A resolution structure of NanoLuc luciferase Deposited 2016-02-22	Different construct 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 28–196（169 aa） Fragment：Full Length	Mutation：A4E, Q11R, Q18L, L27V, A33N, K43R, V44I, A54I, F68D, L72Q, M75K, I90V, P115E, Q124K, Y138I, N166R	DKA DECANOIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% (w/v) PEG 3350, 200 mM ammonium nitrate	Resolution 1.95 Å R-free 0.250
5IBO 1.95A resolution structure of NanoLuc luciferase Deposited 2016-02-22	Different construct 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 28–196（169 aa） Fragment：Full Length	Mutation：A4E, Q11R, Q18L, L27V, A33N, K43R, V44I, A54I, F68D, L72Q, M75K, I90V, P115E, Q124K, Y138I, N166R	DKA DECANOIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% (w/v) PEG 3350, 200 mM ammonium nitrate	Resolution 1.95 Å R-free 0.250
7SNR 2.00A Resolution Structure of NanoLuc Luciferase Deposited 2021-10-28	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 28–196（169 aa）	Mutation：A4E, Q11R, Q18L, L27V, A33N, K43R, V44I, A54I, F68D, L72Q, M75K, I90V, P115E, Q124K, Y138I, N166R Non-standard monomer：Yes (specific site not provided by mmCIF)	ACT ACETATE ION × 2 FLC CITRATE ANION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；1.0 M ammonium citrate dibasic, 0.1 M sodium acetate trihydrate	Resolution 2.00 Å R-free 0.213
7SNR 2.00A Resolution Structure of NanoLuc Luciferase Deposited 2021-10-28	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 28–196（169 aa）	Mutation：A4E, Q11R, Q18L, L27V, A33N, K43R, V44I, A54I, F68D, L72Q, M75K, I90V, P115E, Q124K, Y138I, N166R Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；1.0 M ammonium citrate dibasic, 0.1 M sodium acetate trihydrate	Resolution 2.00 Å R-free 0.213
7SNS 1.55A Resolution Structure of NanoLuc Luciferase Deposited 2021-10-28	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 28–196（169 aa）	Mutation：A4E, Q11R, Q18L, L27V, A33N, K43R, V44I, A54I, F68D, L72Q, M75K, I90V, P115E, Q124K, Y138I, N166R	ACT ACETATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；2.8 M Sodium acetate trihydrate, 0.1 M BIS-TRIS propane	Resolution 1.55 Å R-free 0.189
7SNS 1.55A Resolution Structure of NanoLuc Luciferase Deposited 2021-10-28	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 28–196（169 aa）	Mutation：A4E, Q11R, Q18L, L27V, A33N, K43R, V44I, A54I, F68D, L72Q, M75K, I90V, P115E, Q124K, Y138I, N166R	ACT ACETATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；2.8 M Sodium acetate trihydrate, 0.1 M BIS-TRIS propane	Resolution 1.55 Å R-free 0.189
7SNS 1.55A Resolution Structure of NanoLuc Luciferase Deposited 2021-10-28	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 28–196（169 aa）	Mutation：A4E, Q11R, Q18L, L27V, A33N, K43R, V44I, A54I, F68D, L72Q, M75K, I90V, P115E, Q124K, Y138I, N166R	ACT ACETATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；2.8 M Sodium acetate trihydrate, 0.1 M BIS-TRIS propane	Resolution 1.55 Å R-free 0.189
7SNS 1.55A Resolution Structure of NanoLuc Luciferase Deposited 2021-10-28	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 28–196（169 aa）	Mutation：A4E, Q11R, Q18L, L27V, A33N, K43R, V44I, A54I, F68D, L72Q, M75K, I90V, P115E, Q124K, Y138I, N166R	ACT ACETATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；2.8 M Sodium acetate trihydrate, 0.1 M BIS-TRIS propane	Resolution 1.55 Å R-free 0.189
7SNT 2.20A Resolution Structure of NanoLuc Luciferase with Bound Substrate Analog 3-methoxy-furimazine Deposited 2021-10-28	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 28–196（169 aa）	Mutation：A4E, Q11R, Q18L, L27V, A33N, K43R, V44I, A54I, F68D, L72Q, M75K, I90V, P115E, Q124K, Y138I, N166R	9Z5 (4S)-8-benzyl-2-[(furan-2-yl)methyl]-3-methoxy-6-phenylimidazo[1,2-a]pyrazine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；1.0 M sodium citrate dibasic, 0.1 M Tris, 0.2 M NaCl	Resolution 2.20 Å R-free 0.264
7SNT 2.20A Resolution Structure of NanoLuc Luciferase with Bound Substrate Analog 3-methoxy-furimazine Deposited 2021-10-28	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 28–196（169 aa）	Mutation：A4E, Q11R, Q18L, L27V, A33N, K43R, V44I, A54I, F68D, L72Q, M75K, I90V, P115E, Q124K, Y138I, N166R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；1.0 M sodium citrate dibasic, 0.1 M Tris, 0.2 M NaCl	Resolution 2.20 Å R-free 0.264
7SNW 1.80A Resolution Structure of NanoLuc Luciferase with Bound Inhibitor PC 16026576 Deposited 2021-10-28	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 28–196（169 aa）	Mutation：A4E, Q11R, Q18L, L27V, A33N, K43R, V44I, A54I, F68D, L72Q, M75K, I90V, P115E, Q124K, Y138I, N166R	MG MAGNESIUM ION × 1 SO4 SULFATE ION × 3 9YR 2-(methoxycarbonyl)thiophene-3-sulfonic acid × 1 9Y4 N-[(4-methylphenyl)methyl]-N~2~-phenylglycinamide × 1 GOL GLYCEROL × 1 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；1.8 M Magnesium Sulfate, 0.1 M Bis-Tris Propane	Resolution 1.80 Å R-free 0.175
7SNW 1.80A Resolution Structure of NanoLuc Luciferase with Bound Inhibitor PC 16026576 Deposited 2021-10-28	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 28–196（169 aa）	Mutation：A4E, Q11R, Q18L, L27V, A33N, K43R, V44I, A54I, F68D, L72Q, M75K, I90V, P115E, Q124K, Y138I, N166R	MG MAGNESIUM ION × 1 SO4 SULFATE ION × 1 9YR 2-(methoxycarbonyl)thiophene-3-sulfonic acid × 1 9Y4 N-[(4-methylphenyl)methyl]-N~2~-phenylglycinamide × 1 GOL GLYCEROL × 2 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；1.8 M Magnesium Sulfate, 0.1 M Bis-Tris Propane	Resolution 1.80 Å R-free 0.175
7SNW 1.80A Resolution Structure of NanoLuc Luciferase with Bound Inhibitor PC 16026576 Deposited 2021-10-28	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 28–196（169 aa）	Mutation：A4E, Q11R, Q18L, L27V, A33N, K43R, V44I, A54I, F68D, L72Q, M75K, I90V, P115E, Q124K, Y138I, N166R	MG MAGNESIUM ION × 1 SO4 SULFATE ION × 1 9YR 2-(methoxycarbonyl)thiophene-3-sulfonic acid × 1 9Y4 N-[(4-methylphenyl)methyl]-N~2~-phenylglycinamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；1.8 M Magnesium Sulfate, 0.1 M Bis-Tris Propane	Resolution 1.80 Å R-free 0.175
7SNX 1.70A Resolution Structure of NanoBiT Complementation Reporter Complex of LgBit and SmBiT Subunits Deposited 2021-10-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 28–183（156 aa） Fragment：M-1 to S157 Chain B 185–195（11 aa）	Mutation：;A4E, Q11E, G15A, Q18L, L27V, F31L, A33N, G35A, K43R, V44I, L46R, G51A, A54I, G67A, F68D, G71A, L72Q, M75E, I76V, I90V, H93P, I107L, D108N, P115E, Q124K, Y138I, N144T, L149M, G157S ; Mutation：W161Y, C164F, N166E Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；291 K；1.5 M Na/K Phosphate, 4 (v/v) % 1,3-propanediol	Resolution 1.70 Å R-free 0.178
7SNY 2.10A Resolution Structure of NanoBiT Complementation Reporter Large Subunit LgBiT Deposited 2021-10-28	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 28–183（156 aa） Fragment：M-1 to S157	Mutation：;A4E, Q11E, G15A, Q18L, L27V, F31L, A33N, G35A, K43R, V44I, L46R, G51A, A54I, G67A, F68D, G71A, L72Q, M75E, I76V, I90V, H93P, I107L, D108N, P115E, Q124K, Y138I, N144T, L149M, G157S ;	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；15% (v/v) 2-methyl-2,4-pentanediol, 0.1 M sodium acetate, 2% (w/v) PEG 4000	Resolution 2.10 Å R-free 0.277
8AQ6 NanoLuc luciferase with bound furimamide in surface allosteric site Deposited 2022-08-11	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 28–196（169 aa）	Not recorded	GOL GLYCEROL × 1 PG4 TETRAETHYLENE GLYCOL × 3 OXY OXYGEN MOLECULE × 1 CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；293.15 K；200 mM MgCl2, 100 mM KCl, 25 mM Na acetate pH = 4.0, PEG 400	Resolution 1.69 Å R-free 0.183
8AQ6 NanoLuc luciferase with bound furimamide in surface allosteric site Deposited 2022-08-11	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 28–196（169 aa）	Not recorded	PG4 TETRAETHYLENE GLYCOL × 1 CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；293.15 K；200 mM MgCl2, 100 mM KCl, 25 mM Na acetate pH = 4.0, PEG 400	Resolution 1.69 Å R-free 0.183
8AQ6 NanoLuc luciferase with bound furimamide in surface allosteric site Deposited 2022-08-11	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 28–196（169 aa）	Not recorded	PG4 TETRAETHYLENE GLYCOL × 1 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；293.15 K；200 mM MgCl2, 100 mM KCl, 25 mM Na acetate pH = 4.0, PEG 400	Resolution 1.69 Å R-free 0.183
8AQ6 NanoLuc luciferase with bound furimamide in surface allosteric site Deposited 2022-08-11	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 28–196（169 aa）	Not recorded	CL CHLORIDE ION × 2 PGE TRIETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；293.15 K；200 mM MgCl2, 100 mM KCl, 25 mM Na acetate pH = 4.0, PEG 400	Resolution 1.69 Å R-free 0.183
8AQ6 NanoLuc luciferase with bound furimamide in surface allosteric site Deposited 2022-08-11	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 28–196（169 aa）	Not recorded	PG4 TETRAETHYLENE GLYCOL × 2 CL CHLORIDE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；293.15 K；200 mM MgCl2, 100 mM KCl, 25 mM Na acetate pH = 4.0, PEG 400	Resolution 1.69 Å R-free 0.183
8AQ6 NanoLuc luciferase with bound furimamide in surface allosteric site Deposited 2022-08-11	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 28–196（169 aa）	Not recorded	CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；293.15 K；200 mM MgCl2, 100 mM KCl, 25 mM Na acetate pH = 4.0, PEG 400	Resolution 1.69 Å R-free 0.183
8AQ6 NanoLuc luciferase with bound furimamide in surface allosteric site Deposited 2022-08-11	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain G 28–196（169 aa）	Not recorded	CL CHLORIDE ION × 4 NT0 N-(3-Benzyl-5-phenylpyrazin-2-yl)-2-(furan-2-yl)acetamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；293.15 K；200 mM MgCl2, 100 mM KCl, 25 mM Na acetate pH = 4.0, PEG 400	Resolution 1.69 Å R-free 0.183
8AQ6 NanoLuc luciferase with bound furimamide in surface allosteric site Deposited 2022-08-11	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain H 28–196（169 aa）	Not recorded	GOL GLYCEROL × 1 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；293.15 K；200 mM MgCl2, 100 mM KCl, 25 mM Na acetate pH = 4.0, PEG 400	Resolution 1.69 Å R-free 0.183
8AQH NanoLuc-Y94A luciferase mutant Deposited 2022-08-12	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 28–196（169 aa）	Mutation：Y94A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；293.15 K；MgCl2, KCl, Na acetate, PEG-400	Resolution 2.80 Å R-free 0.305
8AQH NanoLuc-Y94A luciferase mutant Deposited 2022-08-12	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 28–196（169 aa）	Mutation：Y94A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；293.15 K；MgCl2, KCl, Na acetate, PEG-400	Resolution 2.80 Å R-free 0.305
8AQI NanoLuc luciferase with bound coelenteramide in surface allosteric site Deposited 2022-08-12	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 28–196（169 aa）	Not recorded	CEI N-[3-BENZYL-5-(4-HYDROXYPHENYL)PYRAZIN-2-YL]-2-(4-HYDROXYPHENYL)ACETAMIDE × 1 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；293.15 K；MgCl2, KCl, Na acetate, PEG-400	Resolution 1.99 Å R-free 0.207
8AQI NanoLuc luciferase with bound coelenteramide in surface allosteric site Deposited 2022-08-12	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 28–196（169 aa）	Not recorded	CL CHLORIDE ION × 3 PG4 TETRAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；293.15 K；MgCl2, KCl, Na acetate, PEG-400	Resolution 1.99 Å R-free 0.207
8AQI NanoLuc luciferase with bound coelenteramide in surface allosteric site Deposited 2022-08-12	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 28–196（169 aa）	Not recorded	CL CHLORIDE ION × 1 PG4 TETRAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；293.15 K；MgCl2, KCl, Na acetate, PEG-400	Resolution 1.99 Å R-free 0.207
8AQI NanoLuc luciferase with bound coelenteramide in surface allosteric site Deposited 2022-08-12	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 28–196（169 aa）	Not recorded	CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；293.15 K；MgCl2, KCl, Na acetate, PEG-400	Resolution 1.99 Å R-free 0.207
8AQI NanoLuc luciferase with bound coelenteramide in surface allosteric site Deposited 2022-08-12	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 28–196（169 aa）	Not recorded	CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；293.15 K；MgCl2, KCl, Na acetate, PEG-400	Resolution 1.99 Å R-free 0.207
8AQI NanoLuc luciferase with bound coelenteramide in surface allosteric site Deposited 2022-08-12	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 28–196（169 aa）	Not recorded	CL CHLORIDE ION × 2 PG4 TETRAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；293.15 K；MgCl2, KCl, Na acetate, PEG-400	Resolution 1.99 Å R-free 0.207
8AQI NanoLuc luciferase with bound coelenteramide in surface allosteric site Deposited 2022-08-12	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain G 28–196（169 aa）	Not recorded	CEI N-[3-BENZYL-5-(4-HYDROXYPHENYL)PYRAZIN-2-YL]-2-(4-HYDROXYPHENYL)ACETAMIDE × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；293.15 K；MgCl2, KCl, Na acetate, PEG-400	Resolution 1.99 Å R-free 0.207
8AQI NanoLuc luciferase with bound coelenteramide in surface allosteric site Deposited 2022-08-12	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain H 28–196（169 aa）	Not recorded	CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；293.15 K；MgCl2, KCl, Na acetate, PEG-400	Resolution 1.99 Å R-free 0.207
8HCQ Cryo-EM structure of endothelin1-bound ETAR-Gq complex Deposited 2022-11-02	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain R 27–184（158 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.01 Å
8HCX Cryo-EM structure of Endothelin1-bound ETBR-Gq complex Deposited 2022-11-03	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 27–184（158 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
8HNK CXCR3-DNGi complex activated by CXCL11 Deposited 2022-12-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain R 27–184（158 aa）	Not recorded	CLR CHOLESTEROL × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.01 Å
8HNL CXCR3-DNGi complex activated by PS372424 Deposited 2022-12-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 27–184（158 aa）	Not recorded	CLR CHOLESTEROL × 2 4AI (3S)-N-[(2S)-5-carbamimidamido-1-(cyclohexylmethylamino)-1-oxidanylidene-pentan-2-yl]-2-(4-oxidanylidene-4-phenyl-butanoyl)-3,4-dihydro-1H-isoquinoline-3-carboxamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.98 Å
8HNM CXCR3-DNGi complex activated by VUF11222 Deposited 2022-12-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 27–184（158 aa）	Not recorded	CLR CHOLESTEROL × 2 4IE [4-(2-bromophenyl)phenyl]methyl-[[(1R,5S)-6,6-dimethyl-2-bicyclo[3.1.1]hept-2-enyl]methyl]-dimethyl-azanium × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.94 Å
8JPN Cryo-EM structure of succinate receptor bound to cis-epoxysuccinic acid coupling to Gi Deposited 2023-06-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 28–184（157 aa）	Not recorded	U9S (2R,3S)-oxirane-2,3-dicarboxylic acid × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
8K2X CXCR3-DNGi complex activated by CXCL10 Deposited 2023-07-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain R 27–184（158 aa）	Not recorded	CLR CHOLESTEROL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9K07 Cryo-EM structure of the DSO-5a-bound human BRS3-Gq complex Deposited 2024-10-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain R 28–183（156 aa）	Not recorded	A1EL6 [(1~{S})-1-[1,4-dimethoxy-8-nitroso-5-(oxidanylamino)naphthalen-2-yl]-2,2-dimethyl-but-3-enyl] furan-2-carboxylate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.83 Å
9LWP Cryo-EM structure of the unliganded human BRS3-Gq complex Deposited 2025-02-16	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric	Chain R 28–183（156 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.93 Å
9UPU Cryo-EM strucutre of CXCR4 complexed with agonist SDV1a Deposited 2025-04-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain R 32–183（152 aa）	Not recorded	CLR CHOLESTEROL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
9UPV Cryo-EM structure of CXCR4 complexed with agonist SDVX1 Deposited 2025-04-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain R 32–183（152 aa）	Not recorded	CLR CHOLESTEROL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å

21 other PDB entries and 44 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	LUCI_OPLGR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 23–191； UniProt 28–196 Author chain B； PDBConstruct 23–191； UniProt 28–196

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5b0u
Deposition date deposition_date	2015-11-04
Structure title title	Crystal structure of the mutated 19 kDa protein of Oplophorus luciferase (nanoKAZ)
Keywords keywords	Oplophorus luciferase, LUMINESCENT PROTEIN; LUMINESCENT PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	35.24 Å
Radius of gyration Rg (electron density) rg_electron	34.84 Å
Forward intensity I(0) i0	20876600.00
Molecular weight molecular_weight	37979.0 kDa
Excluded volume excluded_volume	48181 Å³
Envelope volume envelope_volume	70234 Å³
Hydration-shell volume shell_volume	16715 Å³
Envelope diameter envelope_diameter	103.6 Å
Shell Rg shell_rg	42.06 Å
Envelope Rg envelope_rg	33.03 Å
Shape Rg shape_rg	34.84 Å
Total Rg total_rg	35.46 Å
Total atoms total_atoms	2688
Residues n_residues	338
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	110.1 Å
Rg (real space) rg_real	35.52 Å
Rg uncertainty (real space) rg_real_error	1.12 Å
I(0) (real space) i0_real	2.0880e+07
I(0) uncertainty (real space) i0_real_error	3.5790e+05
Rg (reciprocal space) rg_reciprocal	35.36 Å
I(0) (reciprocal space) i0_reciprocal	20870000.0000
Solution quality estimate total_estimate	0.6337
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	22.0 Å
Skewness Skewness skewness	0.158
Kurtosis Kurtosis kurtosis	-1.352
Angular range angular_range	— – 0.2250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3361000.0000
Real-space data points n_real_points	46
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.030; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.156; Smooth: 0.989

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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Unit-cell length a length_a	79.067 Å
Unit-cell length b length_b	79.067 Å
Unit-cell length c length_c	123.425 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 42 21 2
Space-group number int_tables_number	94
Crystal system crystal_system	—

Resolution resolution	1.710 Å
Low-resolution limit resolution_low	48.648 Å
R factor r_factor	0.2024
R_work r_work	0.2013
R_free r_free	0.2264

Description description	Oplophorus-luciferin 2-monooxygenase catalytic subunit
Molecular weight formula_weight	21517.5 kDa
Mutation mutation	A4E, Q11R, Q18L, L27V, A33N, K43R, V44I, A54I, F68D, L72Q, M75K,I90V, P115E, Q124K, Y138I, N166R
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3020

Crystal structure of the mutated 19 kDa protein of Oplophorus luciferase (nanoKAZ)

1. Protein Identity and Related Structures Protein Identity & Related Structures

Oplophorus-luciferin 2-monooxygenase catalytic subunit

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Oplophorus gracilirostris
通用名 common_name	Luminous shrimp
NCBI Class编号 ncbi_taxonomy_id	727944
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	332

fit	/app/data/saxs_computation/b0/5b0u/5b0u.fit
pddf	/app/data/pr_computation/b0/5b0u/5b0u.pr.out
profile	/app/data/saxs_computation/b0/5b0u/5b0u.dat