7SNW: PDB entry 7SNW

1.80A Resolution Structure of NanoLuc Luciferase with Bound Inhibitor PC 16026576. Determined by X-ray diffraction at 1.8 Å resolution. Released 16 Nov 2022.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Oplophorus gracilirostris
Chains: 3
Atoms: 4,732
Mol. weight: 60.65 kDa
Ligands: MG, 9YR, 9Y4
Released: 16 Nov 2022

Explore 7SNW in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7SNW contains 15 α-helices and 34 β-strands across 3 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: 5 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	29-37	9
β-strand	41-47	7	1
β-strand	51-61	11	1
α-helix	67-77	11
β-strand	81-84	4	1
β-strand	87-98	12	1
β-strand	104-107	4	1
α-helix	108	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: 5 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	3-6	4
β-strand	8-16	9	2
α-helix	18-22	5
α-helix	29-37	9
β-strand	41-46	6	2
β-strand	51-61	11	2
α-helix	67-77	11
α-helix	80	1
β-strand	81-84	4	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

Chain C: 5 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	3-6	4
β-strand	8-16	9	3
α-helix	18-24	7
α-helix	29-37	9
β-strand	41-47	7	3
β-strand	51-61	11	3
α-helix	67-77	11
β-strand	81-84	4	3
β-strand	87-98	12	3
β-strand	105-107	3	4
α-helix	108	1
β-strand	114-116	3	4
β-strand	117-120	4	3
β-strand	124-130	7	3
β-strand	136-143	8	3
β-strand	149-155	7	3
β-strand	158-166	9	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Oplophorus-luciferin 2-monooxygenase catalytic subunit	A, B, C	protein	174	Oplophorus gracilirostris	Q9GV45 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>7SNW_1 Oplophorus-luciferin 2-monooxygenase catalytic subunit (chains A, B, C)
SDNMVFTLEDFVGDWRQTAGYNLDQVLEQGGVSSLFQNLGVSVTPIQRIVLSGENGLKID
IHVIIPYEGLSGDQMGQIEKIFKVVYPVDDHHFKVILHYGTLVIDGVTPNMIDYFGRPYE
GIAVFDGKKITVTGTLWNGNKIIDERLINPDGSLLFRVTINGVTGWRLCERILA

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	3
9YR	2-(methoxycarbonyl)thiophene-3-sulfonic acid	C6 H6 O5 S2	3
9Y4	N-[(4-methylphenyl)methyl]-N~2~-phenylglycinamide	C16 H18 N2 O	3

Water and common crystallization additives (SO4, GOL, CL) are not listed.

Primary citation

1.80A Resolution Structure of NanoLuc Luciferase with Bound Inhibitor PC 16026576. Encell, L.P., Lovell, S., Mehzabeen, N. 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)
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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