5B0U: Mutated 19 kDa protein of Oplophorus luciferase

Crystal structure of the mutated 19 kDa protein of Oplophorus luciferase (nanoKAZ). Determined by X-ray diffraction at 1.71 Å resolution. Released 13 Jan 2016.

Method: X-ray diffraction
Resolution: 1.71 Å
Organism: Oplophorus gracilirostris
Chains: 2
Atoms: 3,020
Mol. weight: 43.04 kDa
Released: 13 Jan 2016

Explore 5B0U in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5B0U contains 8 α-helices and 22 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	3-6	4
β-strand	8-16	9	1
α-helix	18-24	7
α-helix	30-34	5
β-strand	39-47	9	1
β-strand	51-61	11	1
α-helix	67-77	11
β-strand	81-82	2	1
β-strand	87-98	12	1
β-strand	105-107	3	1
β-strand	114-120	7	1
β-strand	124-130	7	1
β-strand	136-143	8	1
β-strand	149-155	7	1
β-strand	158-166	9	1

Chain B: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	3-6	4
β-strand	8-16	9	2
α-helix	18-25	8
α-helix	30-33	4
β-strand	39-46	8	2
β-strand	51-61	11	2
α-helix	67-77	11
β-strand	81-82	2	2
β-strand	87-98	12	2
β-strand	104-107	4	2
β-strand	114-120	7	2
β-strand	124-130	7	2
β-strand	136-143	8	2
β-strand	149-155	7	2
β-strand	158-166	9	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Oplophorus-luciferin 2-monooxygenase catalytic subunit	A, B	protein	191	Oplophorus gracilirostris	Q9GV45 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5B0U_1 Oplophorus-luciferin 2-monooxygenase catalytic subunit (chains A, B)
MNHKVHHHHHHMELGTLEGSEFFTLEDFVGDWRQTAGYNLDQVLEQGGVSSLFQNLGVSV
TPIQRIVLSGENGLKIDIHVIIPYEGLSGDQMGQIEKIFKVVYPVDDHHFKVILHYGTLV
IDGVTPNMIDYFGRPYEGIAVFDGKKITVTGTLWNGNKIIDERLINPDGSLLFRVTINGV
TGWRLCERILA

Primary citation

Crystal structure of nanoKAZ: The mutated 19 kDa component of Oplophorus luciferase catalyzing the bioluminescent reaction with coelenterazine. Tomabechi, Y., Hosoya, T., Ehara, H. et al. Biochem Biophys Res Commun (2016) 470:88-93. DOI 10.1016/j.bbrc.2015.12.123 · PubMed

Other PDB entries of the same protein (UniProt Q9GV45 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7SNS 1.55 Å, 1.55A Resolution Structure of NanoLuc Luciferase
8AQ6 1.69 Å, NanoLuc luciferase with bound furimamide in surface allosteric site
7VSX 1.7 Å, Crystal structure of QL-nanoKAZ (Reverse mutant of nanoKAZ with L18Q and V27L)
7SNX 1.7 Å, 1.70A Resolution Structure of NanoBiT Complementation Reporter Complex of LgBit and…
7SNW 1.8 Å, 1.80A Resolution Structure of NanoLuc Luciferase with Bound Inhibitor PC 16026576
5IBO 1.95 Å, 1.95A resolution structure of NanoLuc luciferase
8AQI 1.99 Å, NanoLuc luciferase with bound coelenteramide in surface allosteric site
7SNR 2.0 Å, 2.00A Resolution Structure of NanoLuc Luciferase
7SNY 2.1 Å, 2.10A Resolution Structure of NanoBiT Complementation Reporter Large Subunit LgBiT
7SNT 2.2 Å, 2.20A Resolution Structure of NanoLuc Luciferase with Bound Substrate Analog…
9UPV 2.7 Å, Cryo-EM structure of CXCR4 complexed with agonist SDVX1
8AQH 2.8 Å, NanoLuc-Y94A luciferase mutant

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