5IBO: 1.95A resolution structure of NanoLuc luciferase

1.95A resolution structure of NanoLuc luciferase. Determined by X-ray diffraction at 1.95 Å resolution. Released 13 Apr 2016.

Method: X-ray diffraction
Resolution: 1.95 Å
Organism: Oplophorus gracilirostris
Chains: 2
Atoms: 2,670
Mol. weight: 39.2 kDa
Ligands: DKA
Released: 13 Apr 2016

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

Secondary structure: helices and β-sheets

5IBO contains 11 α-helices and 24 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: 6 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	3-6	4
β-strand	8-16	9	1
α-helix	18-23	6
α-helix	28-34	7
β-strand	36-37	2	2
β-strand	41-46	6	1
β-strand	51-61	11	1
α-helix	62-64	3
α-helix	67-77	11
β-strand	81-84	4	1
β-strand	87-98	12	1
β-strand	105-109	5	1
β-strand	112-120	9	1
β-strand	124-130	7	1
β-strand	136-143	8	1
α-helix	148	1
β-strand	149-155	7	1
β-strand	158-166	9	1

Chain B: 5 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	3-6	4
β-strand	8-16	9	2
α-helix	18-24	7
α-helix	31-34	4
β-strand	36-37	2	1
β-strand	41-46	6	2
β-strand	51-61	11	2
α-helix	62-64	3
α-helix	69-76	8
β-strand	81-82	2	2
β-strand	87-98	12	2
β-strand	105-109	5	2
β-strand	114-120	7	2
β-strand	125-130	6	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	174	Oplophorus gracilirostris	Q9GV45 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5IBO_1 Oplophorus-luciferin 2-monooxygenase catalytic subunit (chains A, B)
SDNMVFTLEDFVGDWRQTAGYNLDQVLEQGGVSSLFQNLGVSVTPIQRIVLSGENGLKID
IHVIIPYEGLSGDQMGQIEKIFKVVYPVDDHHFKVILHYGTLVIDGVTPNMIDYFGRPYE
GIAVFDGKKITVTGTLWNGNKIIDERLINPDGSLLFRVTINGVTGWRLCERILA

Ligands and cofactors

ID	Name	Formula	Copies
DKA	Decanoic acid	C10 H20 O2	2

Primary citation

To be determined. Lovell, S., Mehzabeen, N., Battaile, K.P. et al. To be published.

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…
5B0U 1.71 Å, Crystal structure of the mutated 19 kDa protein of Oplophorus luciferase (nanoKAZ)
7SNW 1.8 Å, 1.80A Resolution Structure of NanoLuc Luciferase with Bound Inhibitor PC 16026576
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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